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Victoria Hand is assigned to lead S.H.I.E.L.D.'s efforts to rescue Phil Coulson, while his captors from Centipede Project torture him to learn the secret of his resurrection. Believing Skye to be untrustworthy, and after seeking Melinda May's input, Hand has Skye removed from the Bus. S.H.I.E.L.D. captures Mr. Vanchat, a black market dealer and an associate of Raina's. Ward manages to get Mr. Vanchat to supply S.H.I.E.L.D. with information on her, though a rather unorthodox interrogation. Meanwhile, Skye sets out on her own investigation. She impersonates May to trick and coerce Lloyd Rathman, a businessman of questionable dealings, to assist her into hacking into secured files.
Coulson is initially tortured by Edison Po, who tells him that the Clairvoyant couldn't glean the information they wanted because the Clairvoyant had been unable to sense Coulson since his resurrection. The Clairvoyant decides that Po's methods are ineffective, and kills him, after which Raina takes over Coulson's interrogation. She uses a scanning device to compel him to remember aspects of his being brought back to life. Coulson experiences flashbacks in which a reluctant Dr. Streiten and others operate on him. During the flashbacks, Coulson's skull cap is removed and his brain directly stimulated by a robotic apparatus, while Coulson begs to be allowed to die.
Coulson's team rescues him, after which he confronts Streiten, who tells Coulson he had been dead for days, not minutes, and was resurrected at the orders of Director Nick Fury. Streiten reveals that after his revival, Coulson had lost the will to live, and that the doctors manipulated Coulson's brain to give him false memories and restore him to the man he was before.
Meanwhile, Mike Peterson is alive, albeit badly burned, missing the lower half of his right leg, and now possessing an explosive surveillance eye implanted in him by someone working for the Clairvoyant.
- Clark Gregg as Agent Phil Coulson
- Ming-Na Wen as Agent Melinda May
- Brett Dalton as Agent Grant Ward
- Chloe Bennet as Skye
- Iain De Caestecker as Agent Leo Fitz
- Elizabeth Henstridge as Agent Jemma Simmons
- Saffron Burrows as Agent Victoria Hand
- Rob Huebel as Lloyd Rathman
- J. August Richards as Michael Peterson
- Ruth Negga as Raina
- Cullen Douglas as Edison Po
- Ron Glass as Doctor Streiten
- Aiden Turner as Vanchat
- Felisha Terrell as Emily Deville
- Samantha Cutaran as Karine
- Imelda Corcoran as Doctor Goodman
- Darren Dupree Washington as Interrogating Agent
- David Lim as Waiter
- Christopher Rocha as Tow Truck Driver
- Justin Gant as PD Guard #1
- Wayne Alon Scott as PD Guard #2
- Matt Mullins as Centipede Soldier 2
- Adam Lytle as Centipede Soldier 3
- Gabriel Koura as Centipede Soldier 1 (uncredited)
- Alice Chen as S.H.I.E.L.D. Agent (uncredited)
- Sun Jae Kim as Scientist (uncredited)
- Samuel L. Jackson as Nick Fury (uncredited stock-footage cameo)
- Los Angeles, California
- Mojave Desert
- The Guest House
- Bethesda, Maryland
- Key Largo, Florida (mentioned)
- Cayman Islands (mentioned)
- Sydney, Australia (mentioned)
- Geneva, Switzerland (mentioned)
- New York City, New York (mentioned)
- The Fridge (mentioned)
- S.H.I.E.L.D. Headquarters (mentioned)
- Flash Bomb
- Tracking Bracelet
- Theta Brain-Wave Frequency Machine
- Memory Overwriting Machine
- Backscatter X-Ray Eye Implant
- Night-Night Bracelet
- Night-Night Pistol (mentioned)
- Jasper Sitwell
- Ace Peterson
- Robert Coulson
- Nick Fury (mentioned & archive footage)
- Maria Hill
- Chan Ho Yin
- Akela Amador
- Audrey Nathan
- David Rathman
- President Matthew Ellis
- Julie Coulson
- Doctor Nugent
- Michael Jordan
- Bryon Russell
- Tiny Wings
- The method the Clairvoyant uses to kill Edison Po is similar to the Sonic Taser used by Obadiah Stane in Iron Man.
- Leo Fitz references the catchphrase "Embrace the Change", used to promote the Secret Invasion event in the comics.
- Skye being called "Doctor Nugent" by Jemma Simmons when she phoned after being expelled from the team is most likely a reference to Alice Nugent.