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S.H.I.E.L.D was co-founded by Howard Stark and possibly Nick Fury more than twenty years before the events involving the creation Iron Man armor. S.H.I.E.L.D. wishes to debrief Tony Stark about his escape from Afghanistan and arrests Obadiah Stane for planning the kidnap and murder of Stark as well as dealing weapons to terrorists. It also provides a cover story for what happened at Stark Industries during Iron Man and Iron Monger's fight, a story that Stark does not stick to instead revealing his secret to the world.

S.H.I.E.L.D. recruits Tony Stark as a consultant for the Avenger Initiative and organizes Senator Stern to present Tony Stark and James Rhodes with their medals. S.H.I.E.L.D. sends agent Coulson to New Mexico to find Mjolnir. Meanwhile, Phil Coulson and Jasper Sitwell discuss how to stop General Ross releasing Emil Blonsky and to decide Tony Stark. General Ross enlists the help of S.H.I.E.L.D. to help him track Bruce Banner's e-mails to "Mr. Blue".

Agent Coulson of S.H.I.E.L.D. stops a robbery in a gas station while on his way to Mjolnir. S.H.I.E.L.D. had taken all of Jane Foster's research. Thor fights with some of Agent Coulson's men before being captured and interrogated by Coulson about his identity, origin and training. Mjolnir is also kept in a S.H.I.E.L.D. facility. Loki send The Destroyer to attack Thor and S.H.I.E.L.D. agents, after The Destoryer was defeated Thor told Coulson to return Jane's work and in return Coulson could count on Thor's help when needed. In a post-credits scene, Dr. Selvig is taken to a S.H.I.E.L.D. facility where he meets Nick Fury. Fury asks Selvig to study the recently-discovered Cosmic Cube, which holds untold power, to which Selvig agrees. It is then revealed that Selvig is under the control of Loki, who has been transported to Earth.

S.H.I.E.L.D. scientists in the Arctic uncover Captain America's frozen body in The Red Skull's airship from WWII. Rogers awakens in a room designed to appear as if he were still in the early 1940s. Deducing the truth and escaping to Times Square, Rogers learns from S.H.I.E.L.D. leader Nick Fury that he has been asleep for nearly 70 years, and they had wanted to acclimate his reentry into modern times. In a deleted scene it is revealed that S.H.I.E.L.D. was once called the Strategic Scientific Reserve.

S.H.I.E.L.D. is directly responsible in forming the Avengers as a deterrent against Loki's plans and to help get the Tessaract back into S.H.I.E.L.D. custody. However Tony Stark, Bruce Banner and Captain America find out that S.H.I.E.L.D. want the Tesserect in order to make weapons (similar to the way HYDRA did in World War II). Many S.H.I.E.L.D. agents watch on monitors as the Avengers fight the Chitauri in New York. In the end, S.H.I.E.L.D. Director Nick Fury tells his Superiors (known simply as The Council) that he has allowed custody of the Tesserect to go to Thor who has taken it back to Asgard and that the remaining Avengers have gone their separate ways and that they are no longer answering to S.H.I.E.L.D.

Nick Fury

Assistant Director:
Maria Hill

Phil Coulson
Jasper Sitwell
Victoria Hand
Steve Rogers
Clint Barton
Natasha Romanoff
Felix Blake
John Garrett
Antoine Triplett
Agent 13
Melinda May
Grant Ward
Leo Fitz
Jemma Simmons
Eric Koenig
Billy Koenig
Sam Koenig
Mike Peterson
Benjamin Pollack
Claire Wise
Sam Rollins
Typical S.H.I.E.L.D. Agent

The Triskelion
The Hub
The Slingshot
The Fridge
The Sandbox
S.H.I.E.L.D. Trauma Zentrum
The Cube
The Treehouse
S.H.I.E.L.D. Academy
S.H.I.E.L.D. Academy of Science and Technology (sieged by HYDRA)
S.H.I.E.L.D. Training Facility
The Guest House
The Coventry

Vehicles and Equipment:
S.H.I.E.L.D. Helicarrier No. 64
Project Insight Helicarrier
The Iliad
S.H.I.E.L.D. Quinjets
CXD 23 Airborne Mobile Command Station
S.H.I.E.L.D. Motorcycle
S.H.I.E.L.D. Jump Jet
S.H.I.E.L.D. Helicopter
Various S.H.I.E.L.D. Weapons
Various S.H.I.E.L.D. Equipment