| "It's our policy not to comment on ongoing operations, but I can assure you that S.H.I.E.L.D. has the situation completely under control."|
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- "Banner's work was very early phase. It wasn't even weapons application. He thought he was working on radiation resistance. I would never have told him what the project really was. But he was so sure of what he was onto, that he tested it on himself. And something went very wrong. Or it went very right. As far as I'm concerned, that man's whole body is the property of the US Army."
- ―LTG Ross
This is a timeline of events that occurred during the 2000s.
- New Year's Day comes, and the distraught Aldrich Killian is still waiting for Tony Stark on the roof of a building in Bern, Switzerland, because Stark promised to meet him there. Meanwhile, Stark chose to party and sleep with Maya Hansen. Seeing the New Year's celebrations below inspires Killian to continue his work without Stark. That morning, Maya Hansen wakes up to find Stark has discreetly left her.
- Aldrich Killian accepts Maya Hansen into A.I.M., and they continue to develop the Extremis virus.
- Bill Clinton's presidency comes to an end. His time in office was influenced by elements of HYDRA. 
- NASA sends an astronaut, Will Daniels, and three scientists, Taylor, Brubaker, and Austin, through the Monolith to survey the planet on the other side of the portal until an extraction team could come to retrieve them.
- After the 9/11 attacks, Thaddeus Ross convinces the US Military to create the Bio-Tech Force Enhancement Project, based on Project Rebirth in World War II.
- Eight thousand members of Iraq's 51st Infantry Division surrender to US and UK forces, however, it is orchestrated by HYDRA.
- Having been accepted into Columbia University Law School, Matt Murdock, aged 19, arrives in his room and introduces himself to his new roommate Foggy Nelson, meeting him as he manages to sign on to a Punjabi course at the last minute. Nelson had heard of what had happened to Murdock as a child, and is excited for their upcoming three years together.
- John Garrett returns to Grant Ward five years after leaving him in the Wyoming wilderness. He tells Ward he has been accepted into S.H.I.E.L.D. and will operate within it as a sleeper agent for HYDRA.
- Bruce Banner joins the Bio-Tech Force Enhancement Project at Culver University at the insistence of his girlfriend Betty Ross. Betty's father, General Thaddeus Ross lies to the scientists on the project, claiming their work will help protect soldiers from depleted uranium.
- Under the threat of funding cuts, Bruce Banner tests the Bio-Tech Force Enhancement Project on himself, but the combination of Gamma Radiation and the serum Betty Ross developed based on Abraham Erskine's Super Soldier Serum results in the accident that turns him into Hulk. Gamma pulses stored in Banner's amygdala and released during high stress moments trigger each transformation. Betty is injured and hospitalized.
- Bruce Banner visits Betty Ross at the hospital and Thaddeus Ross admits to Banner that the project is being developed as weapon, not just defense. Banner goes on the run. The Military closes the lab building for a year and shuts down the Bio-Tech Force Enhancement Project. General Ross keeps some project data, while Betty also secretly holds onto data and remains at Culver University. After Banner's leak, Ross put the military in his track. Angered by her father's treatment of Banner, Betty stops talking to him.
- Bruce Banner tries to flee from the United States and into Canada by sneaking into a truck that was heading through the border with Idaho. Banner is caught but when the State Troopers officers try to arrest him, Banner is forced to transform into Hulk.
- Hulk flees after the incident. In his run, the Hulk is sighted by locals along the US/Canada border.
- After the incident, a watch is found with the words "To Bruce, all my love, Betty" inscribed on the back of it.
- Bruce Banner tries to contact Betty Ross, but the e-mail is intercepted by the Military and she never receives it. 
- The Mossad sends a photograph of a destructive event, possibly linked to Hulk, to the Strategic Operations Command Center.
- The Lion King musical moves from the New Amsterdam Theater to the Minskoff Theatre in New York City.
- Murdock and Nelson gatecrash an expensive party together, and there Murdock meets fellow student Elektra Natchios. As the two of them talk, Natchios deduces things about him, however, Murdock uses his wit to keep the conversation going, and the two leave the party together, getting into another person's sports car and driving off. From then on, the two continue to commit reckless acts together and get closer.
- Late at night, Matt Murdock and Elektra Natchios break into Fogwell's Gym. The two of them discuss their pasts and learn more about each other, with both also mentioning that they have enjoyed the last few weeks together. They begin to playfully fight in the boxing ring, but the intimacy leads the two of them passionately making love in that gym for the first time.
- Akela Amador and two other S.H.I.E.L.D. agents conduct a raid to one of Vanchat's gulags. The agents are murdered and Amador is captured, spending four years in a cage.
- Agent Phil Coulson of S.H.I.E.L.D. sends a second team to the gulag raided by Akela Amador's team. They find several corpses, but do not locate Amador.
- Attack on Roscoe Sweeney: In the night, Natchios takes Murdock to an expensive penthouse. They break in and go to the kitchen, taking food from the fridge and discussing the passionate and luxurious future that the two of them want to have together. When they hear noises, Natchios goes ahead of Murdock, and when he walks into the room, she gleefully tells him that she has Roscoe Sweeney, the killer of Murdock's father, bound to a chair for him to enact revenge on. This was his house all along, and she expected him to appreciate the gesture. Murdock is at first reluctant, but Natchios manipulates him to start punching Sweeney. Because of her, he begins to savor the feeling of revenge. However, when she then tries to get him to kill Sweeney, Murdock realizes what a dangerous relationship he has got himself into. He steps away, breaking off his relationship with Natchios, and calls the police; however when he looks around, Natchios is gone.
- With their finals fast approaching after nearly 3 years of law school, having now developed a strong friendship, Nelson often jokes about Murdock's blindness, while Murdock would tease Nelson about many of his poor life choices, such as his decision to join a course studying Punjabi simply to get close to a girl. On a night out together when they really should be studying, Nelson asks Murdock what happened to "the Greek girl" who Murdock was dating, to which Murdock simply replies that things did not work out. The two joke about their future as partners at law, and they swear to work together for many years.
- The Military loses Bruce Banner, who eventually arrives in Eastern Nunavut near Greenland, in the Arctic Circle to commit suicide in a place where his body would not be found.
- In the Arctic, Banner tries to shoot himself in the mouth. The attempt fails and he turns into Hulk, who spits out the bullet, and Banner wakes up afterwards. The incident is detected by satellite, and this is the last sighting of Bruce Banner for at least five months.
- A picture that came to the United States Armed Forces of a wrecked car in Samara, Russia is assigned as a possible incident caused by Hulk.
- S.H.I.E.L.D. is brought in to help Thaddeus Ross, and continues helping him until 2011. Stark Industries sells him HMMWV-mounted sonic cannons.
- Nick Fury, in disguise, finds Bruce Banner in a bar and tries to find out what Thaddeus Ross' "Super-Soldier Program" did to him. He tells Agents Johnson and Peterson to gain Banner's trust and see how he reacts to certain things, so the agents pretend they were dating and Johnson cheated on Peterson with him. Banner gets confused when Johnson pulls him toward her, and Peterson threatens him. The stress of the situation causes Banner to turn into Hulk and go on a rampage.
- Nick Fury calls a meeting of S.H.I.E.L.D. operatives and tells them Hulk is only a secondary matter.
- Aldrich Killian injects himself with Extremis, which heals his disabilities and enables him to walk without a cane.
- Escape from Utkin Prison: Using the bones of their dead cellmate Alexei as weapons, Anatoly and Vladimir Ranskahov escape from Utkin Prison. Their original plan was to return to Moscow where they once lived as princes, but they instead travel to New York City to forge a new life.
- Eva Belyakov, a member of the Inhuman community in Afterlife, goes rogue after Jiaying refuses to allow Belyakov's unstable daughter, Katya, to go through Terrigenesis. She takes with her an assortment of stolen Terrigen Crystals, which she uses to transform Katya without the proper mental conditioning. Katya develops sensory manipulating powers and a hunger for pain. The mother-daughter duo travel to Bahrain, where they create chaos by using Katya's powers to sap the emotional energies from local civilians.
- Rescue in Bahrain: S.H.I.E.L.D. takes notice of the Belyakovs' activities and tracks Eva down to Manama, Bahrain. A team led by Phil Coulson and Melinda May is dispatched to analyze Belyakov for the Index; they are unaware of Katya's involvement or powers. Eva and Katya assume control of a group of gangsters and hold the entire S.H.I.E.L.D., minus Coulson and May, hostage within a warehouse. May ventures into the warehouse alone and crosses off the controlled gangsters and Eva. Katya reveals herself to May and nearly uses her powers to kill the subjugated S.H.I.E.L.D. team, forcing May to shoot her dead. For her role in saving them, the S.H.I.E.L.D. team gives May the nickname "The Cavalry", a moniker she grows to despise.
- Jiaying and Gordon travel to Manama with the intention of dealing with Eva and Katya themselves, but find that S.H.I.E.L.D. has already killed them.
- May returns to the United States, traumatized by the ordeal in Manama. She shuts herself off from everyone, including her husband Andrew Garner. Their marriage over time falls apart. With approval from Maria Hill, May switches from field duty to a simple desk job.
- Aldrich Killian finds candidates for his Extremis program, including Ellen Brandt, Chad Davis, Eric Savin, and Jack Taggart, all of whom were in the United States Army and suffered serious injuries.
- The candidates are given Extremis. Some of them do not survive, and their bodies explode. The successful subjects heal from their injuries and regrow lost limbs.
- Natasha Romanoff is given the task of escorting a nuclear scientist out of Iran. The Winter Soldier attacks them in Odessa, Ukraine, firing a bullet which goes through Romanoff's abdomen and hits the scientist, successfully killing him.
- Nick Fury puts Phil Coulson in charge of Project T.A.H.I.T.I., an experiment in which the preserved corpse of the Kree that was recovered in 1945 is harvested of its bodily fluids for medicinal purposes. The goal of the project is to create a medicine that could potentially save a mortally wounded Avenger.
- Chad Davis explodes from an Extremis malfunction in Rose Hill, Tennessee. Five other people are killed in the explosion.
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Iron Man 3
- ↑ Luke Cage: 1.02: Code of the Streets
- ↑ 3.0 3.1 3.2 3.3 Captain America: The Winter Soldier
- ↑ Agents of S.H.I.E.L.D.: 3.05: 4,722 Hours
- ↑ Agents of S.H.I.E.L.D.: 4.02: Meet the New Boss
- ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 6.11 The Incredible Hulk
- ↑ 7.0 7.1 Agents of S.H.I.E.L.D.: 1.02: 0-8-4
- ↑ Avengers: Age of Ultron
- ↑ 9.0 9.1 Daredevil: 1.10: Nelson v. Murdock
- ↑ Agents of S.H.I.E.L.D.: 1.21: Ragtag
- ↑ Historical character's date of death.
- ↑ Agents of S.H.I.E.L.D.: 4.02: Meet the New Boss
- ↑ 13.0 13.1 Daredevil: 1.04: In the Blood
- ↑ Agents of S.H.I.E.L.D.: 2.03: Making Friends and Influencing People
- ↑ 15.0 15.1 15.2 15.3 The Incredible Hulk: The Big Picture
- ↑ Agents of S.H.I.E.L.D.: 4.07: Deals With our Devils
- ↑ 17.0 17.1 The Avengers
- ↑ 18.0 18.1 18.2 Daredevil: 2.05: Kinbaku: "10 Years Ago".
- ↑ 19.0 19.1 Agents of S.H.I.E.L.D.: 1.04: Eye-Spy
- ↑ 20.0 20.1 The Incredible Hulk Extended Scene
- ↑ 21.0 21.1 The Incredible Hulk: The Fury Files
- ↑ Agents of S.H.I.E.L.D.: 4.02: Meet the New Boss
- ↑ 23.0 23.1 23.2 23.3 Agents of S.H.I.E.L.D.: 2.17: Melinda: "7 Years Ago".
- ↑ Agents of S.H.I.E.L.D.: 2.02: Heavy is the Head
- ↑ Ant-Man
- ↑ Agents of S.H.I.E.L.D.: 1.07: The Hub
- ↑ Agents of S.H.I.E.L.D.: 1.20: Nothing Personal
- ↑ Agents of S.H.I.E.L.D.: 3.08: Many Heads, One Tale
- ↑ Captain America: Civil War Prelude