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- "Attention all S.H.I.E.L.D. agents, this is Steve Rogers. You've heard a lot about me over the last few days. Some of you were even ordered to hunt me down. But I think it's time to know the truth. S.H.I.E.L.D. is not what we thought it was. It's been taken over by HYDRA. Alexander Pierce is their leader. The STRIKE and Insight crew are HYDRA as well. I don't know how many more, but I know they're in the building. They could be standing right next to you. They almost have what they want: absolute control. They shot Nick Fury, and it won't end there. If you launch those Helicarriers today HYDRA will be able to kill anyone that stands in their way... unless we stop them. And I know I'm asking a lot. The price of freedom is high, it always has been. And it's a price I'm willing to pay. And if I'm the only one, then so be it. But I'm willing to bet I'm not."
- ―Captain America
This is a timeline of events that occurred in 2014.
- Under Kilgrave's influence, Jessica Jones kills Reva Connors. Jones rebels against Kilgrave's control and leaves Kilgrave, who is hit by a bus.
- Having almost been killed in the accident, Kilgrave searches the help of Doctor David Kurata and forces Jack Denton to donate both of his kidneys to him. Kurata is forced to perform the surgery on Kilgrave without any anesthesia to numb the pain, because the anesthesia nullifies Kilgrave's powers. Denton has a stroke from the shock of losing his kidneys. Kilgrave then ensures that his death has been faked and disappears, while Jessica Jones continues to believe that he died in the accident.
- Edison Po is broken out of Havenworth Federal Penitentiary by Brian Hayward and other Centipede Soldiers.
- Needing help tracking down the Centipede Project, Phil Coulson travels to a S.H.I.E.L.D. Training Facility to recruit new S.H.I.E.L.D. trainee Michael Peterson.
- Coulson's Team tracks down Laura Hayward and traces her cell phone call to Brian to Oakland, California.
- Ambush on Oakland Centipede Base: Coulson, Peterson, Melinda May and Grant Ward lead an attack on the facility, not knowing that three Centipede soldiers were in cargo bins waiting to strike. They were deployed to attack the S.H.I.E.L.D. agents. Peterson gets stabbed by a stick causing him severe damage, but despite the injury, he manages to subdue Hayward. May also takes another Centipede soldier down, but he manages to escape with another soldier. Before being interrogated, Hayward is killed using his Backscatter X-Ray Eye Implant.
- Kidnapping of Phil Coulson: Michael Peterson is persuaded by Coulson to call his son and Raina answers the telephone, wanting Peterson to trade Coulson for Ace's safety.
- Peterson is presumed killed by S.H.I.E.L.D. when he is caught in the explosion that the Centipede Project ignited to facilitate their escape with the captive Coulson.
- Coulson's Team, with Victoria Hand as the superior agent, helps in the capture of Vanchat.
- Skye is evicted from the Bus by Hand, following advice from Melinda May. She then goes to Los Angeles, steals Lloyd Rathman's car, enters his home, and, with the help of Rathman and his security guards, accesses Rathman's computer to find the Centipede Project. 
- Raina takes control of Phil Coulson's interrogation after Edison Po is killed by the Clairvoyant.
- Coulson is persuaded by Raina to use the Theta Brain-Wave Frequency Machine to see what happened during his resurrection. He discovers that Tahiti was a memory implant caused by the Memory Overwriting Machine and Karine transforms into Dr. Goodman, the assistant of Dr. Streiten.
- Coulson's Team raids the Mojave Desert hideout holding Coulson and captures Raina.
- Michael Peterson awakens to learn that he is missing a leg, his eye has been replaced with a Backscatter X-Ray Eye Implant, and that he now works for the Clairvoyant. 
- Captain America and Black Widow thwart the Cadre's kidnapping attempt on Professor Sana Amanat in Brooklyn. While there, Steve remembers growing up in the area.
- Kidnapping of Trevor Slattery: Posing as a documentary film maker, Ten Rings agent Jackson Norriss visits Trevor Slattery in Seagate Prison and interviews him about how he became involved with Aldrich Killian. Killing the guards, Norriss reveals he has been ordered to take Slattery to the Mandarin, who is a real terrorist leader and not a fabrication of Killian's as Slattery assumed.
- With the help of Callie Hannigan, Grant Ward and Skye figure out that Donnie Gill is using Leo Fitz to help him create an Atmospheric Moisture Freezing Device for Ian Quinn.
- Donnie Gill and Seth Dormer create a super storm using an Atmospheric Moisture Freezing Device they have completed. Dormer is killed by a lightning strike. Gill is arrested and taken to the Sandbox, while demonstrating a freezing power.
- Ian Quinn gets a call from Phil Coulson. During that call, Quinn tells Coulson that the Clairvoyant says hello.
- The Daily Cadet, the student newspaper of the S.H.I.E.L.D. Academy of Science and Technology, runs a front page article about Jemma Simmons and Leo Fitz saving Donnie Gill.
- Coulson's Team goes to Jamaica, tipped off by John Garrett, to find a mysterious weapon that is connected to Ian Quinn. There, Grant Ward and Melinda May fight the weapon's guards but they escape with help from Phil Coulson.
- Leo Fitz and Jemma Simmons learn that the weapon is Chitauri-inspired but augmented with Overkill technology.
- Coulson's Team boards a train traveling from Verona to Zagreb because it carries a package that Ian Quinn bought and is being protected by Cybertek-hired mercenaries.
- Michael Peterson is removed from a Hyperbaric Chamber and fitted with a new prosthetic leg, before he kills Sofia and the other Cybertek employees who delivered it.
- Infiltration into Ian Quinn's Villa: Skye is shot twice in the abdomen by Quinn. Coulson's team raids Quinn's mansion and places Skye in the hyperbaric chamber.
- Ian Quinn is arrested by Coulson's team.
- Skye is taken to Zurich, Switzerland to see Dr. Jazuat in S.H.I.E.L.D. Trauma Zentrum.
- Garrett's Team boards the Bus after Coulson's team fails to release Quinn to the Fridge.
- Raid of the Guest House: Coulson finds a room marked T.A.H.I.T.I. and is surprised to discover the corpse of an alien marked G.H. that is being drained of its bodily fluids.
- The Guest House is destroyed as Skye is miraculously healed by GH.325.
- Chase of Lorelei: Lorelei arrives in Death Valley, stopping at a roadside in where she enthralls newlywed Jimmy Mackenzie. Mackenzie drives Lorelei to Rosie's Desert Oasis in Nevada. There, Lorelei abandons and kills Mackenzie in favor of a local biker gang, the Dogs of Hell.
- The Dogs of Hell, led by Rooster, begin a string of robberies to appease Lorelei.
- Loki under the guise of Odin, orders Sif to go to Earth and apprehend Lorelei.
- S.H.I.E.L.D. detects Sif's arrival in Death Valley and send Coulson's Team there to meet her. After relaying information about Lorelei to them, Sif allies with the team to capture her. Phil Coulson asks Sif about what other extraterrestrial races she has encountered, hoping to discover what alien G.H. is.
- Lorelei enthralls the local law enforcement to act as her protection, and is tracked to Rosie's Desert Oasis by S.H.I.E.L.D. The enthralled distract both S.H.I.E.L.D. and Sif away from Lorelei, who enthralls Grant Ward to aid in her getaway.
- Lorelei and Ward arrive in Las Vegas, where she and Ward have sex after discussing plans for Lorelei's takeover.
- Sif and Coulson track Lorelei to Vegas, but find that she and Ward have already escaped.
- In order to rid themselves of Sif and S.H.I.E.L.D., Lorelei and Ward infiltrate the Bus by enthralling Leo Fitz, who detains Skye, Jemma Simmons, and Sif, even attempting to eject Sif from the plane. Coulson, pretending to be under Lorelei's thrall, releases Skye and Simmons and incapacitates Fitz. May fights with the enthralled Ward, while Sif manages to get back onto the Bus and duels Lorelei. Sif manages to overpower Lorelei and places the Asgardian Collar around her, silencing her. The enthralled are released from Lorelei's control almost instantly.
- Sif returns Lorelei to Asgard.
- Phil Coulson reveals to Skye that the GH.325 came from a Kree corpse, and promises that they will find the answers they need about Project T.A.H.I.T.I. After eavesdropping on the conversation, Melinda May calls Nick Fury from the Bus on a secret phone, telling him that Coulson knows about the alien.
- S.H.I.E.L.D. agents Nicholas Cooper and Mark Smith try to discover the importance of the Scepter in the S.H.I.E.L.D. S.T.A.T.I.O.N..
- Agent Mark Smith goes to the gym so he can take his anger out on a punching bag. When he finishes and goes to the locker room for his duffel bag, he discovers a paper inside simply saying "Hangar SFC-5".
- Smith arrives in the hangar and is greeted by Baron Wolfgang von Strucker, who recruits him into HYDRA.
- Nicholas Cooper discovers during a lunch break that the connection between the Scepter and the Tesseract is much simpler than he originally thought. But just as he makes the discovery, his former colleague, Mark Smith, shoots and kills him. Now a HYDRA operative, Smith takes the Scepter and begins to transport it to Wolfgang von Strucker with the help of Mark Basso.
- In Sokovia, a massive riot for justice breaks out, putting civilians against the police. During this riot, the Scepter is finally delivered to Wolfgang von Strucker, who immediately puts Doctor List to work.
- Doctor List manages to reactivate Chitauri Guns with the power of the Scepter for HYDRA. After the guns are tested, List informs Strucker that they need living human test subjects. Strucker tells him that he can use any of the people from the continuing riot.
- List tells the rioters that he can give them the abilities to stand up to their oppressors if they volunteer to go with him. Twins Pietro and Wanda Maximoff are among the many to go with him.
- List begins work on the Maximoff twins, excited to see the successful results of his experiments on the twins, following many failures. Subjection to the Scepter's energy gives the twins supernatural powers: Pietro gains super speed, while Wanda obtains telekinesis and energy projection.
- Search for the Clairvoyant: Phil Coulson attends a meeting with Jasper Sitwell, Victoria Hand, Felix Blake, John Garrett and his team to discuss the possible identities of the Clairvoyant. Sitwell is later ordered to report to the S.H.I.E.L.D. ship Lemurian Star.
- Skye becomes a level one agent of S.H.I.E.L.D..
- In Washington, D.C., Steve Rogers meets former soldier Sam Wilson on his morning jog. They discuss the difficulties of adapting to life after active service, and Wilson recommends Rogers listen to Marvin Gaye's "Trouble Man" album.
- Natasha Romanoff picks Rogers up and briefs him about their latest mission: rescuing hostages from the Lemurian Star, a S.H.I.E.L.D. ship which has been hijacked by Algerian pirates, led by Georges Batroc.
- Hijacking and Retaking of the Lemurian Star: That evening, Captain America and the Black Widow join agents of S.H.I.E.L.D. subdivision STRIKE as they recapture the Lemurian Star and rescue the hostages. After fighting the pirate leader Georges Batroc, Captain America discovers the Black Widow extracting data from the ship's computers, an element of the mission he was not informed about.
- At the Triskelion (S.H.I.E.L.D.'s headquarters in Washington, D.C.), Steve Rogers confronts Nick Fury about keeping certain parts of the rescue mission secret from him. Fury shows him S.H.I.E.L.D.'s latest endeavor: Project Insight, three Helicarriers connected to orbital satellites and designed to preemptively eliminate potential threats. However, Rogers finds this project morally questionable.
- Rogers goes to the Smithsonian Institution's Captain America exhibit and reminisces about his time in World War II. He then visits Peggy Carter, who is now nearly 93 years old, in a retirement home.
- Sam Wilson hosts a counseling session for war veterans with post-traumatic stress disorder. Rogers attends and listens to the testimony of a veteran named Garcia and Wilson's speech. 
- Melinda May receives a message that Nick Fury is at the Triskelion.
- Deathlok critically injuries Felix Blake during the hunt for the Clairvoyant.
- Nick Fury tries to read the data the Black Widow extracted from the Lemurian Star's computers, but to his surprise he is denied access. He informs Alexander Pierce of this, and requests Project Insight be postponed due to his underlying suspicions.
- Attack on Nick Fury: Fury leaves the Triskelion and contacts Maria Hill to arrange a meeting. On the way to the rendezvous point, he is attacked by assassins posing as police officers. He evades them, but is confronted by the Winter Soldier, who shoots a Magnetic Disk Grenade under Nick Fury's SUV, forcing it to upturn. Severely injured, Fury escapes by using a "Mouse Hole" device to cut through the road and into the sewers. Steve Rogers returns to his apartment, where he finds Fury sitting in his living room. Fury manages to tell Rogers that S.H.I.E.L.D. has been compromised and gives him the USB containing the data from the Lemurian Star. From the adjacent building, the Winter Soldier shoots and appears to fatally wound Fury. While his neighbor (who reveals herself to be an undercover S.H.I.E.L.D. agent codenamed "Agent 13") gets Fury to safety, Rogers pursues the Winter Soldier, but fails to catch him.
- Nick Fury is taken to a hospital in a critical condition. His heart stops during surgery, and the doctors are unable to revive him. After he is pronounced dead, Maria Hill collects his body. Rogers hides the USB Fury gave him in a vending machine.
- Believing Steve Rogers may be withholding information from S.H.I.E.L.D., Alexander Pierce questions him about the circumstances of Nick Fury's death. Rogers does not tell him about the USB or anything Fury said to him before he was shot. Pierce reveals that Fury hired Georges Batroc to hijack the Lemurian Star, and Natasha Romanoff's extraction of data from the computers was the real mission.
- Chase of Captain America: On his way back to the hospital to retrieve the USB, Rogers is attacked by several STRIKE operatives in an elevator, but manages to defeat all of them. He jumps out of the elevator to avoid arrest, drives away on his motorcycle and evades an attacking Quinjet. Pierce tells the rest of S.H.I.E.L.D. that Rogers is now a wanted fugitive and must be hunted down.
- Rogers returns to the hospital, but the USB is no longer in the vending machine. Natasha Romanoff reveals that she has it, and explains who the Winter Soldier is.
- At an Apple computer store, Rogers and Romanoff try to read the data on the USB. While the information itself is inaccessible, they manage to trace back the location where the program was first written: a S.H.I.E.L.D. bunker in New Jersey. STRIKE operatives led by Brock Rumlow search for the fugitives, but do not find them.
- In Pensacola, Florida, Grant Ward kills Thomas Nash, a reject of the Index, when he threatens Skye. Ward is taken into custody on the Bus.
- Stealing a car, Rogers and Romanoff drive to the location and he recognizes it as Camp Lehigh, the military training camp where he trained during World War II. In the bunker, they find an old supercomputer, and, inserting the USB, they reactivate the preserved consciousness of Arnim Zola. Zola explains that HYDRA has continued to operate within S.H.I.E.L.D. since its creation in the 1940's, and several S.H.I.E.L.D. operatives including Alexander Pierce, Jasper Sitwell and Brock Rumlow are actually sleeper agents for HYDRA. The information on the USB is an algorithm Zola produced for Project Insight. Before Rogers and Romanoff can get any more information from him, a S.H.I.E.L.D. fighter jet bombs the bunker, destroying the computers. Surviving the explosion, they once again evade S.H.I.E.L.D. capture.
- At his home, Alexander Pierce is visited by the Winter Soldier, and sets him a mission to terminate the fugitives. Renata witnesses the exchange and is killed by Pierce.
- Battle of Washington, D.C.: Steve Rogers and Natasha Romanoff seek refuge at Sam Wilson's home. He agrees to help them, and reacquires the EXO-7 Falcon flight harness he used while serving in the army. They abduct Jasper Sitwell and interrogate him about the nature of Project Insight. He reveals Arnim Zola's algorithm will seek out any individual or group that poses a threat to HYDRA. The Insight Helicarriers will then eliminate the targets, placing a majority of the East Coast at risk. The Winter Soldier attacks, kills Sitwell and battles Rogers. During the fight, Rogers removes the Winter Soldier's mask and recognizes him as Bucky Barnes. A S.H.I.E.L.D. team soon arrives and arrests Rogers, Romanoff, and Wilson.
- Maria Hill, disguised as an escort, rescues Rogers, Romanoff, and Wilson, and takes them to Nick Fury, who faked his death by means of an anti-stress serum created by Bruce Banner. They formulate a plan to stop Project Insight using three special computer chips that will reroute the Helicarriers' targeting system, forcing them to destroy each other.
- In order to establish a line of communication with Jemma Simmons, who has been transferred to the Hub as a consultant on Deathlok, Leo Fitz creates a hidden phone line but discovers the hidden phone line of Melinda May.
- Victoria Hand takes control of the Bus and sets it to dock with the Hub, believing Phil Coulson and his team may be part of a conspiracy within S.H.I.E.L.D.
- Agent Hand sends two S.H.I.E.L.D. UAVs to kill John Garrett, whom she suspects along with Coulson of being part of the same conspiracy. Garrett manages to evade his attackers and docks with the Bus.
- With his suit damaged, Rogers breaks into the Smithsonian Institution and steals a 1940s Captain America costume on display.
- Battle at the Triskelion: Alexander Pierce invites the World Security Council to the Triskelion to show them a demonstration of Project Insight. Captain America infiltrates the headquarters and reveals the nature of Project Insight and the HYDRA infiltration to everyone present. Pierce takes the Council hostage, but Black Widow, disguised as Councilwoman Hawley, defends them and holds Pierce at gunpoint. She and Fury then upload all data regarding S.H.I.E.L.D. and HYDRA to the public, and Fury executes Pierce after he kills the Council in an attempt to escape. Captain America and Sam Wilson, going by the codename Falcon, board the Helicarriers as they take off and manage to install two of the chips.
- On the last Helicarrier, Captain America is confronted by the Winter Soldier, and after a brutal altercation, Captain America manages to install the chip. The Helicarriers target each other and blow each other out of the sky; the Helicarrier holding Rogers and the Winter Soldier crashes into the Triskelion, reducing it to rubble. The Winter Soldier, slowly remembering his past life as Bucky Barnes, saves Captain America from drowning in the Potomac River.
- HYDRA sends out a coded message to all of its agents, ordering them to take direct control of S.H.I.E.L.D. Skye decodes the message, leading the the team to conclude that Hand is the Clairvoyant and affiliated with HYDRA.
- Exposed to the public, HYDRA begins purging all infiltrated S.H.I.E.L.D. facilities in an attempt to retain control. The Cube and S.H.I.E.L.D. Academy are among the targeted facilities.
- Battle at the S.H.I.E.L.D. Academy: Anne Weaver, the director of the Academy, is contacted by Jemma Simmons and Antoine Triplett as HYDRA invades the S.H.I.E.L.D. Academy. She warns them about the HYDRA infiltration before the connection is lost. During the battle, HYDRA release an Enhanced person. Weaver fights the Enhanced by herself, but then Tomas Calderon saves her and more students with his Quinjets squadron. 
- Battle at the Hub: The Bus lands at the Hub, where Garrett soon reveals that he is the Clairvoyant and an agent of HYDRA. Coulson's team are nearly killed by Garrett, but Agent Hand, having heard the exchange, saves them. All HYDRA agents present in the Hub are then detained.
- Battle at the Sandbox: Donnie Gill, a victim of the Faustus method, is used by HYDRA as a one-man army to take the Sandbox.
- Hand informs Isabelle Hartley that the Battle at the Hub is over.
- Coulson and Hand watch footage of Project Insight as they assess the losses of S.H.I.E.L.D.
- Victoria Hand and Grant Ward escort John Garrett to the Fridge for incarceration, but midflight, Agent Hand was killed by Ward, revealing him to be Garrett's fellow HYDRA mole.
- Battle on the Iliad: HYDRA forces aboard the S.H.I.E.L.D. aircraft carrier Iliad begin executing loyal S.H.I.E.L.D. operatives. The Lead HYDRA Agent of the attack watches footage of Project Insight before killing Tim Maguire. Acting on orders from Nick Fury, Agents Bobbi Morse and Isabelle Hartley rescue Alphonso Mackenzie and Robert Gonzales. Together, they make their way to the bridge where Morse attempts to extract classified material from the ship's computers, though this places the remaining S.H.I.E.L.D. agents onboard at risk. Having second thoughts, Morse resigns from her initial orders and works with her fellow agents in reclaiming the ship from HYDRA. Now acting solo, the S.H.I.E.L.D. agents aboard the Iliad decide to start a new S.H.I.E.L.D. under Gonzales' command.
- The Winter Soldier goes to the Ideal Federal Savings Bank, where he finds two HYDRA scientists. He claims that Captain America is dead, but then attacks the scientists, feeling that they are responsible for the terrible actions he has done. However, when one man states that he has a daughter, the Winter Soldier lets him go, realizing that he wants no more blood on his hands.
- Grant Ward releases Raina from S.H.I.E.L.D custody.
- Skye and Coulson watch the news as they assess the secured bases of S.H.I.E.L.D..
- Grant Ward and Raina arrive at the Barbershop Headquarters in Havana, Cuba. Here Raina meets the Clairvoyant for the first time and discovers he has no powers.
- In the Hub, Coulson's Team repair the Bus. While doing this, Phil Coulson receives a message from Glenn Talbot.
- S.H.I.E.L.D is declared a terrorist organization by the United States government.
- After receiving the message from Glenn Talbot, Coulson decides to leave the Hub. On the Bus, Skye deletes the identity of every member on their team, including Ward.
- Skye informs Ward that his identity has been deleted and Garrett instructs Raina to recreate the drug GH.325.
- Phil Coulson discovers Nick Fury's coordinates to Providence.
- Agent Kaminsky and others arrive in Cuba after being defeated at another S.H.I.E.L.D. facility. Garrett decides to hit the Fridge.
- May tells Coulson that Fury wasn't behind Project T.A.H.I.T.I..
- Raid of the Fridge: John Garrett and Grant Ward arrive at the Fridge and steal the 0-8-4 from Peru, the Gravitonium, the Berserker Staff, and Donnie Gill's icing machine. They also release from the Fridge many prisoners, including Marcus Daniels and Ian Quinn.
- Coulson's Team finds Providence and meets Eric Koenig. Here they are informed that the Fridge has been taken by HYDRA. Skye calls Ward, because she is worried about him, giving him the coordinates of Providence.
- Raina tells Ward and Garrett that the hard drive cannot be accessed without Skye's pass codes. Garrett sends Ward to obtain the pass codes or Skye herself.
- Maria Hill applies for a job at Stark Industries and is accepted.
- Grant Ward arrives at Providence, where he lies to the team about what happened at the Fridge and gives Skye the hard drive. Ward suggests to back it up now that they are at a secure facility, but Coulson wants her to first pull up a list of all the inmates at the Fridge.
- Ian Quinn arrives in Cuba and is presented with the Gravitonium by Garrett.
- 200 miles out of Portland, Marcus Daniels kills a fisherman so he can use his car to travel to Portland.
- After seeing Marcus Daniels on the list, Coulson decides to take a splinter team to capture him. Before they are allowed to leave the facility they have to go through an orientation on a Lie Detector.
- Daniels arrives in Portland where he goes after Audrey Nathan, his obsession. Before he could get to her she is saved by Jemma Simmons and Antoine Triplett, while Leo Fitz uses his D.W.A.R.F.s to capture him. This does not work.
- In Providence Skye tries to track the other freed prisoners, when she has the idea to hack a NSA satelite to get visuals on them.
- In Portland Fitz comes with the idea to use Audrey Nathan to draw Daniels.
- When Ward plans to kill Melinda May he noticed she is leaving the facility. He then goes after Koenig to kill him.
- In Canada, May is picked up by her mother Lian and she starts her search for Maria Hill.
- Ambush at the Outdoor Theater: On an outside stage Audrey starts playing the cello, drawing Blackout to her. Coulson and his team defeat him.
- Skye uses a tracking system to search for Eric Koenig. She finds his body in a storage room, after which she writes down a message for Coulson, saying Ward is HYDRA.
- The Bus is taken by Grant Ward who wants Skye to give up access codes to Coulson's Team Hard Drive.
- When Coulson and his team return at Providence they notice that the facility is empty and the Bus is gone.
- Natasha Romanoff goes to government hearings about the downfall of S.H.I.E.L.D.
- Maria Hill goes to Senate hearings about the downfall of S.H.I.E.L.D. As she leaves, she is confronted by Melinda May.
- Nick Fury talks to Captain America before leaving for Europe.
- Captain America and Falcon begin their search for the Winter Soldier.
- At a cafe, Grant Ward tries to obtain the codes from Skye, but she reveals that she already knows that Ward is a HYDRA agent and tries to flee, only to be captured by Deathlok who was sent by Garrett to help Ward with Skye.
- While attempting to make pancakes, Jemma Simmons finds the body of Eric Koenig. Simultaneously, Leo Fitz finds the message "Ward Is HYDRA" inscribed in a window of Providence.
- Attack on Providence: Maria Hill leads Glenn Talbot to Providence, but later she helps Coulson and his team escape from Talbot.
- Melinda May recovers the hard drive of Project T.A.H.I.T.I. from Coulson's fake grave.
- Deathlok threatens to kill Ward by cardiac arrest if Skye doesn't deliver the codes of the hard drive.
- Skye delivers the codes to Ward and Deathlok but installs a trojan horse in the drive.
- Phil Coulson rescues Skye using Lola.
- Phil Coulson learns from Melinda May that he was the one who was in charge of Project T.A.H.I.T.I.
- Deathlok kills drug lord Alejandro Castillo. Coulson's Team watches footage on the morning news.
- Coulson and his team arrive at Cybertek Corporate Headquarters and discover that John Garrett was the first Deathlok and that he plans to use the Centipede Serum to cure his own disabilities and to create an army of Deathloks.
- Fitz and Simmons find the Bus, but are captured by Ward and taken to Garrett. Fitz nearly kills Garrett by the use of an EMP but he and Simmons are forced to take refuge in a Medical Pod. Ward finds the two and ejects it into the sea.
- Raina injects Garrett with synthesized GH.325 which heals his failing organs and gives him superhuman strength but starts to give him a psychotic personality.
- Ian Quinn bargains with representatives of the United States Armed Forces in Washington, D.C. about the creation of an army of Deathlok Soldiers for the Military.
- Ambush at the Barbershop Headquarters: Coulson's Team arrive at the Barbershop Headquarters in Cuba but are ambushed by Centipede-enhanced soldiers controlled by Cybertek and Kaminsky, wielding the Berserker Staff. They use the Trojan horse computer program to discover the location of the Cybertek Manufacturing Facility.
- Raina declares to John Garrett that she is not in league with HYDRA. She is only interested in new ways of evolution.
- Leo Fitz and Jemma Simmons are rescued from the sea by Nick Fury, who sends them to the Playground for recovery.
- Battle at Cybertek: Garrett kills one of the generals in attendance at Ian Quinn's presentation of the Deathlok soldiers. Raina and Quinn abandon the Cybertek facility, taking the Gravitonium with them, while Coulson's Team invade Cybertek with a group of U.S. Marines. Grant Ward tries to capture Skye, but Melinda May defeats him in a fight and he is taken into custody. Phil Coulson battles Garrett, but is outmatched. Fury arrives to aid Coulson, while Deathlok steps in to defend Garrett. Skye releases Ace Peterson, prompting Deathlok to turn on Garrett and fire a missile at him. The remaining Centipede agents are arrested, and Deathlok flees the scene. Garrett tries to upgrade himself with Deathlok parts, but Coulson vaporizes him with the 0-8-4 Weapon.
- Fury appoints Coulson as the new director of S.H.I.E.L.D. and gives him a small device called "the Toolbox", which shows him coordinates to their new base, the Playground.
- Upon arriving at the base, the team meet Agent Billy Koenig, the identical twin brother of Eric Koenig.
- Coulson starts to experience the same side effects of the GH.325 that affected Garrett, rewriting the same symbols Garrett wrote.
- Raina visits Calvin Zabo and tells him that she had found his daughter, Skye.
- At the secret HYDRA facility where Loki's Scepter is being held, Wolfgang von Strucker assures the personnel that their work will continue in spite of HYDRA's recent loss at the Triskelion. As he observes Pietro and Wanda Maximoff practicing their abilities, Strucker comments that the "Age of Miracles" has begun.
- At the Captain America Exhibition, in the Smithsonian Institution, The Winter Soldier finds out who he really is, James Barnes.
- Rosalind Price is transferred to the Washington, D.C. branch to serve as a special adviser to Congress.
- Felix Blake is released from hospital. Having found out about HYDRA, he disappears, angered that the S.H.I.E.L.D. he signed up for was not what he thought it to be. Bitter, he looks to find other people to align himself with who want to protect the world from aliens.
- Six months after the supposed death of Kilgrave, Trish Walker finally finds out that her adopted sister, Jessica Jones, has become a private investigator.
- The Nova Empire and the Kree Empire sign a peace treaty, stopping the ongoing war between the two. Ronan the Accuser refuses to submit to the treaty and becomes a terrorist, repeatedly terrorizing Xandarian space.
- The Ravagers are hired by a Xandarian merchant called the Broker to recover the Orb from the planet Morag.
- Battle of Morag: In an attempt to separate from the Ravagers, Star-Lord travels to Morag alone and recovers the Orb, but is attacked by Korath the Pursuer and his Sakaaran mercenaries. They chase Quill off-planet. Quill then makes contact with Yondu Udonta and informs him of his separation. Yondu then orders a bounty on Quill's head.
- Ronan murders a Xandarian Nova Corps operative that had been sent by Irani Rael to negotiate a ceasefire.
- Korath informs Ronan the Accuser of Quill's taking of the Orb, and sends Gamora to retrieve it, not realizing that she is actually working for the Collector.
- Attack on Peter Quill: Star-Lord travels to Xandar and attempts to give the Orb to the Broker, but upon learning that Ronan the Accuser seeks it for himself, the Broker cancels the deal. Gamora attacks Quill and makes off with the Orb. Two criminals, Rocket Raccoon and Groot, attempt to capture Quill to collect Yondu Udonta's bounty, and they, Quill, and Gamora are all apprehended by the Nova Corps and imprisoned on the Kyln.
- Gamora is nearly killed by vengeful inmates led by Drax the Destroyer, whose wife and daughter were murdered by Ronan, but is saved by Quill. Upon learning that the Collector is willing to pay a substantial amount for the Orb, Quill, Rocket, and Groot agree to help Gamora escape the Kyln in exchange for splitting the payment between the four of them.
- Yondu Udonta and the Ravagers visit the Broker, who reveals to them the nature of the Orb.
- Ronan the Accuser is summoned by Thanos to discuss Gamora's desertion. Ronan kills the Other and berates Thanos for not taking the situation seriously. Thanos ignores Ronan's insults and threatens to destroy him if he does not bring him the Orb. Nebula replaces Gamora as Ronan's assistant in the crusade.
- Escape from the Kyln: Star-Lord, Gamora, Rocket Raccoon, and Groot stage a mass breakout on the Kyln. Assisted by Drax the Destroyer, they shut down the prison's power, triggering emergency containment procedures, and then hijack the prison's watchtower, where they shut down the artificial gravity and pilot the watchtower to the prison's hanger bay via hacked security drones. They reclaim the Orb and escape in Quill's ship, the Milano, but Quill remains behind to recover his walkman headset. He manages to regroup with the others, and they flee from the system.
- Ronan and Nebula invade the Kyln but find that Gamora has already fled. Before leaving, Ronan orders for the prison to be "cleansed".
- Skirmish on Knowhere: The Milano arrives at Knowhere, where Gamora schedules a meeting with the Collector. While waiting, the group spend time in the Boot of Jemiah, where Drax, Rocket, and Groot bet on Orloni fights. Star-Lord makes advances towards Gamora, who violently rejects him. Drax and Rocket, both drunk, get into a fight, after which Drax storms off and the rest of the group are summoned by the Collector. They give the Orb to him and he opens it, revealing the Infinity Stone inside. After explaining the stone's origins, the Collector prepares to give the group their payment. His slave, Carina, grabs the stone in order to free herself from slavery, but the power overwhelms and kills her. A massive explosion destroys the Collector's Museum, and Gamora reseals the stone into the Orb. Ronan, Nebula, and their Sakaaran allies are summoned to Knowhere by a vengeful Drax, who is subdued in battle with Ronan. Nebula pursues Gamora into space, leaving her stranded and nearly killing her. While Ronan and his minions make off with the Orb, and Star-Lord contacts the Ravagers to pick up him and Gamora, giving her his helmet to survive.
- After leaving Knowhere, Ronan contacts Thanos and betrays him, deciding to keep the Infinity Stone for himself, grafting it into his hammer. Nebula chooses to remain with Ronan out of spite for Thanos.
- On Knowhere, Groot convinces Rocket to rescue Star-Lord and Gamora.
- On the Eclector, Star-Lord and Gamora negotiate a truce with the Ravagers, agreeing to give the Orb to them if they help them stop Ronan from using it to destroy Xandar. Rocket, Groot, and Drax suddenly arrive and threaten to destroy the mothership with a Hadron Enforcer, but Star-Lord is able to stop him. Star-Lord's group and the Ravagers formulate a plan to hijack Ronan's ship, the Dark Aster, and kill him.
- Star-Lord contacts Nova Corps officer Rhomann Dey and warns him of Ronan the Accuser's attack. Dey forwards the news to Nova-Prime Irani Rael, who prepares Xandar's defenses.
- Battle of Xandar: The Dark Aster arrives at Xandar, and the entire Nova Corps fleet is sent in to intercept it. A Ravager fleet led by Yondu Udonta arrives, distracting the Aster. The Milano, carrying Star-Lord, Gamora, Groot, and Drax the Destroyer, slips through the chaos and infiltrates the Aster. Rocket Raccoon, piloting the Warbird, aids the Nova Corps and Ravagers in dealing with the Sakaarans. The Nova Corps fleet sets up a force shield to keep the Aster from landing. All Sakaaran ground and air forces are subdued, but Ronan, using the Infinity Stone inside the Orb, decimates the entire Nova Corps fleet, including Denarian Garthan Saal. Onboard the Dark Aster, Gamora duels Nebula, who escapes on a hijacked M-ship. Drax kills Korath the Pursuer and Groot slays the rest of the Sakaaran soldiers, and the group then converge on Ronan, who defeats them with ease. Rocket pilots the Warbird through the Aster and into Ronan, incapacitating him and damaging the vessel and causing it to crash into Xandar. Groot shields his comrades in a cocoon of branches to protect them from the crash, and is pulverized in the impact. Ronan emerges from the wreckage unscathed and prepares to destroy Xandar with the Infinity Stone, but Star-Lord distracts him, allowing Rocket and Drax to destroy his hammer with the Hadron Enforcer, freeing the stone. Star-Lord catches the stone and, with Gamora, Rocket, and Drax sharing its burden, uses it to destroy Ronan. Gamora then seals the stone in a new makeshift container, and instead of giving it to the Ravagers, Star-Lord gives them a decoy. The stone is then taken by the Nova Corps and contained.
- Star-Lord's group receive medical attention, and Star-Lord's alien ancestry is revealed.
- Star-Lord's group, now calling themselves the Guardians of the Galaxy, are exalted for their heroics and their criminal records are expunged. Departing in a repaired Milano, the group depart Xandar in search of adventure. They bring a sapling cut of Groot with them, which begins to regenerate.
- On Knowhere, a downtrodden Collector is licked by the dog Cosmo and mocked by one of his old collections, Howard the Duck.
- Without revealing that he has been doing the same, Phil Coulson gives Skye the assignment of translating the Words of Creation that were written on the Bus by John Garrett. During her investigation, she contacts Rising Tide, but they cannot help her.
- Phil Coulson, Melinda May and Skye record a birthday message video for Jemma Simmons for her 27th birthday, as she is not at the base with them, instead on an assignment for Coulson at HYDRA. They tell her to make a wish and then blow out the candle for her. Leo Fitz, still believing that Simmons left to see her parents, records a more personal message, asking her to say "hi" to her parents for him, and promising her that they will see each other soon.
- Brock Rumlow awakes from his coma. He watches a report on the fall of S.H.I.E.L.D. from his hospital bed. Disillusioned and furious at HYDRA's defeat and Alexander Pierce's death, he assaults his nurse and escapes.
- Recovering some items from S.H.I.E.L.D.'s Research and Development labs, Brock Rumlow sets up an arms sale to draw out HYDRA agents, on whom he opens fire to send the message that he no longer works for them, while getting some satisfaction by subjecting them to the pain that he suffered himself.
- Phil Coulson has another episode where he is driven to carve strange symbols on the wall, which Melinda May records for him.
- Phil Coulson leaves the Playground to travel, looking for people across the globe who remain loyal to S.H.I.E.L.D.
- Phil Coulson tells Melinda May that he is on a recruiting trip to London, but instead secretly meets with Sam Koenig in the United States to discuss Theta Protocol, a project created after the collapse of S.H.I.E.L.D., to repair Helicarrier No. 64. Koenig mentions that Simmons is settling in at HYDRA, and Coulson tells him the Skye is doing well in her training with May, Antoine Triplett is now fully on the team and Leo Fitz is making a little progress. They also discuss the new recruits Lance Hunter, Isabelle Hartley and Idaho. He also asks for Koenig to keep looking for Robert Gonzales, who they believe is highly likely to be dead.
- Phil Coulson sends the group of mercenaries he has recently become involved with, (Lance Hunter, Isabelle Hartley and Idaho) to Alexandria, Virginia to buy a file from Roger Browning that contains information about the Obelisk, a mysterious artifact that HYDRA is looking for.
- The negotiation is interrupted by an assassin who kills Browning and escapes.
- Glenn Talbot gives an interview, saying that S.H.I.E.L.D. and HYDRA are enemies of the United States of America and that he will do anything to defeat them.
- Coulson returns to the Playground and tells May about his supposed recruiting trip. He sends Skye to get information from their prisoner, Grant Ward. Ward tells her the history of Carl Creel and how HYDRA is communicating with him. She leaves before he can discuss her father.
- Creel attacks Glenn Talbot, but he is saved by Skye and Melinda May. As Creel is detained by the United States Armed Forces, May and Skye take Talbot to the Playground.
- Coulson tries to force Talbot to reveal information. He refuses and Coulson resorts to his back-up plan and knocks him out with an I.C.E.R..
- Creel uses his powers to become transparent and escape from his detainment.
- Infiltration into the Government Storage Warehouse: Coulson sends a team on a two-pronged mission: to obtain a Quinjet and retrieve the Obelisk. When Hartley finds the Obelisk, the Absorbing Man attacks. She grabs the object in order to defend herself, but instead it begins to kill her. Hartley, Hunter and Idaho attempt to escape to get Hartley medical attention, but Creel flips their S.H.I.E.L.D. SUV, killing both Idaho and Hartley. Hunter fakes being dead as Creel takes the alien artifact.
- Later, Sunil Bakshi approaches Daniel Whitehall to tell him that Creel was successful.
- Melinda May finds Idaho, Isabelle Hartley, and Lance Hunter's flipped SUV. Only Hunter has survived. Hunter tells May to pursue the Absorbing Man. While May chases Creel, Hunter is surrounded and taken by the United States Armed Forces.
- May tracks Creel to a restaurant. In the restaurant, Creel is accidentally touched by a waitress, and she turns to stone. Creel escapes the scene.
- At the Playground, Skye and Antoine Triplett arrive back in the newly acquired Quinjet as they learn of the deaths of Hartley and Idaho. Alphonso Mackenzie looks over the jet's cloaking technology so it can be duplicated for the Bus.
- Hunter is collected by Glenn Talbot, who asks him to betray Phil Coulson because there is a senator who wants his arrest. Hunter wants Hartley to have an honorable funeral in return. Hunter tells Talbot that in return for a proper burial for Hartley and two million dollars, he will hand over Coulson in the next two days.
- When Hunter returns to the Playground, Coulson already knows that Hunter has talked to Talbot. He sends Skye to pack the deceased's possessions.
- Fitz finds the DNA file on the Absorbing Man and decides that he will help in his capture. Mackenzie helps a struggling Fitz to decode his old work to find a solution.
- In the night, Raina visits Creel and gives him a ring that will help him fight against the adverse effects that the Obelisk is having on him. However, unbeknownst to him, the ring contains a tracking device. Raina contacts Coulson and tells him about the tracking device.
- Chase of Carl Creel: Coulson's men track Creel and travel to his location to catch him. Hunter, however, takes things into his own hands and incapacitates May, Triplett and Skye with an I.C.E.R.. When Creel goes to meet Sunil Bakshi in a public park to deliver the Obelisk, Hunter tries to shoot Creel. During the commotion caused by the gunshot, Raina takes the briefcase containing the artifact. As Hunter and Creel battle, Coulson uses the Overkill Device to destabilize and neutralize the Absorbing Man.
- At Hartley's funeral, Hunter decides to join S.H.I.E.L.D.
- Later, Skye and May discuss Coulson's attitude. May confronts Coulson and convinces him to release his urge to carve Words of Creation he has resisted for 18 days since his last episode. He carves the symbols in a blackened room as May documents the incident.
- Raina delivers the Obelisk to Skye's father, who shows her that she can touch it without dying.
- Coulson delivers Creel to Talbot.
- Agent Jemma Simmons, undercover within HYDRA per Phil Coulson's request, goes to her new workplace in HYDRA Laboratories.
- In the Playground, Coulson alerts Melinda May that HYDRA have captured Agent 33.
- Simmons discovers that HYDRA is looking for Donnie Gill, whom she knows from their previous encounter, and that they are studying his abilities.
- In Marrakech, Gill is found by two HYDRA agents. He freezes one of them and takes his cell phone.
- Simmons meets with Coulson and tells him about Gill, and that she believes he must have gained some kind of powers after he was struck by lightning. Coulson decides that they must try to recruit Gill before HYDRA reaches him.
- Skye tries to get information from Grant Ward. Ward tells her that he was never loyal to HYDRA, only to Garrett. He also tells her about HYDRA's protocol when it concerns the "gifted", which is to either recruit or kill them.
- Donnie Gill goes to a freighter. He stands near it and freezes the water.
- Sunil Bakshi accuses Simmons of lying for not telling him that she knew about Project Blizzard, the project that gave powers to Gill. She covers by saying that she did not know who the subject of the project was until yesterday, which is true. Bakshi asks if she is loyal to HYDRA, to which Simmons simply replies that she is loyal to science.
- Coulson and his team hear about the frozen ship in the sea. They prepare to leave on the Bus.
- Bakshi brings together a group of agents with Simmons to go and find Gill.
- Fitz is shocked when he enters Grant Ward's cell. Ward tries to explain himself to Fitz, to no avail. Furious, Fitz explains what Ward has done to him, and starts draining the oxygen from his cell. Ward tells him that Coulson and the others do not understand that Gill was brainwashed and was used by HYDRA to take the Sandbox in one of the battles during the HYDRA Uprising. Fitz tells Mack about Gill and that they have to alert Coulson.
- Battle on the Maribel del Mar: At the freighter, Mack calls Coulson and tells him about Gill being brainwashed by HYDRA. Coulson orders his team to stop HYDRA from talking to Gill to prevent the brainwashing from being triggered again. When May notices Simmons, she takes out Hunter so as to prevent him from killing her, as he does not know who she is. Alerted by the noise, Gill runs. Coulson orders his team to maintain Simmons' cover. Gill runs into Bakshi, who speaks the brainwashing code to him and Gill falls under his sway. Bakshi orders Gill to freeze the ship, but he is shot by Skye. Gill falls into the ocean.
- Skye monitors channels, trying to learn if someone has found Gill's body. Skye tells May that she does not understand why Coulson did not tell anyone about Simmons, but May simply states that she will handle it.
- Coulson goes to talk to Fitz, reminding him that he is still an important part of the team, but that he saw what he did to Ward. Fitz says that he is not a killer. Coulson explains that he hates Ward as much as him, but they need to find out more about HYDRA from him. Coulson reveals to him that Simmons is on assignment, and that is why she has made no contact. He also tells Fitz that is a lot more he is hiding.
- Whitehall tells Bakshi that S.H.I.E.L.D. is becoming a problem and he wants to know who is in charge. Agent 33 then reveals herself, now brainwashed and loyal to Whitehall.
- Ward reveals to Skye that her father is still alive and he wants to meet with her.
- The connection between government conspiracies and S.H.I.E.L.D. is discussed on WHiH World News.
- ↑ Jessica Jones: 1.03: AKA It's Called Whiskey
- ↑ 2.0 2.1 Jessica Jones: 1.02: AKA Crush Syndrome
- ↑ 3.0 3.1 3.2 3.3 3.4 3.5 Agents of S.H.I.E.L.D.: 1.10: The Bridge
- ↑ 4.0 4.1 4.2 4.3 4.4 4.5 Agents of S.H.I.E.L.D.: 1.11: The Magical Place
- ↑ Captain America: Homecoming
- ↑ Marvel One-Shot: All Hail the King
- ↑ 7.0 7.1 7.2 7.3 Agents of S.H.I.E.L.D.: 1.12: Seeds
- ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 Agents of S.H.I.E.L.D.: 2.03: Making Friends and Influecing People
- ↑ 9.0 9.1 Agents of S.H.I.E.L.D.: The Chase
- ↑ 10.0 10.1 10.2 10.3 10.4 Agents of S.H.I.E.L.D.: 1.13: T.R.A.C.K.S.
- ↑ 11.0 11.1 11.2 11.3 11.4 Agents of S.H.I.E.L.D.: 1.14: T.A.H.I.T.I.
- ↑ 12.0 12.1 12.2 12.3 12.4 12.5 12.6 12.7 12.8 12.9 Agents of S.H.I.E.L.D.: 1.15: Yes Men
- ↑ 13.0 13.1 13.2 13.3 13.4 13.5 13.6 13.7 13.8 Avengers: Age of Ultron Prelude - This Scepter'd Isle
- ↑ 14.0 14.1 14.2 14.3 14.4 14.5 Agents of S.H.I.E.L.D.: 1.16: End of the Beginning
- ↑ 15.00 15.01 15.02 15.03 15.04 15.05 15.06 15.07 15.08 15.09 15.10 15.11 15.12 15.13 15.14 15.15 15.16 15.17 15.18 15.19 15.20 15.21 Captain America: Civil War Prelude
- ↑ 16.00 16.01 16.02 16.03 16.04 16.05 16.06 16.07 16.08 16.09 16.10 16.11 16.12 16.13 16.14 16.15 16.16 16.17 16.18 16.19 16.20 16.21 16.22 16.23 16.24 Captain America: The Winter Soldier
- ↑ 17.0 17.1 17.2 17.3 17.4 17.5 17.6 17.7 Agents of S.H.I.E.L.D.: 1.17: Turn, Turn, Turn
- ↑ 18.0 18.1 18.2 Agents of S.H.I.E.L.D.: 2.15: One Door Closes
- ↑ 19.0 19.1 19.2 Captain America: Civil War Prelude Infinite Comic
- ↑ 20.00 20.01 20.02 20.03 20.04 20.05 20.06 20.07 20.08 20.09 20.10 20.11 20.12 20.13 Agents of S.H.I.E.L.D.: 1.18: Providence
- ↑ 21.00 21.01 21.02 21.03 21.04 21.05 21.06 21.07 21.08 21.09 21.10 Agents of S.H.I.E.L.D.: 1.19: The Only Light in the Darkness
- ↑ 22.0 22.1 22.2 22.3 22.4 22.5 22.6 22.7 22.8 Agents of S.H.I.E.L.D.: 1.20: Nothing Personal
- ↑ 23.0 23.1 23.2 23.3 23.4 23.5 Agents of S.H.I.E.L.D.: 1.21: Ragtag
- ↑ 24.0 24.1 24.2 24.3 24.4 24.5 24.6 Agents of S.H.I.E.L.D.: 1.22: Beginning of the End
- ↑ Agents of S.H.I.E.L.D.: 2.09: Ye Who Enter Here
- ↑ Agents of S.H.I.E.L.D.: 3.01: Laws of Nature
- ↑ Agents of S.H.I.E.L.D.: 3.14: Watchdogs
- ↑ Jessica Jones: 1.01: AKA Ladies Night
- ↑ 29.00 29.01 29.02 29.03 29.04 29.05 29.06 29.07 29.08 29.09 29.10 29.11 29.12 29.13 29.14 29.15 29.16 29.17 29.18 29.19 Guardians of the Galaxy
- ↑ 30.00 30.01 30.02 30.03 30.04 30.05 30.06 30.07 30.08 30.09 30.10 30.11 Agents of S.H.I.E.L.D.: 2.01: Shadows
- ↑ Agents of S.H.I.E.L.D.: 3.05: 4,722 Hours
- ↑ 32.00 32.01 32.02 32.03 32.04 32.05 32.06 32.07 32.08 32.09 32.10 32.11 Agents of S.H.I.E.L.D.: 2.02: Heavy is the Head
- ↑ Agents of S.H.I.E.L.D.: 2.20: Scars
- ↑ WHiH Newsfront Google+ Posts