S.H.I.E.L.D. (Strategic Homeland Intervention, Enforcement Logistics Division) was a worldwide military organization, and its duty was to protect the world. Its headquarters was the flying aircraft carrier called the S.H.I.E.L.D. Helicarrier.
They appeared when the Living Laser took over a S.H.I.E.L.D. space station and Nick Fury warned Iron Man not to interfere with their plan to reclaim it from the Laser. After a space assault failed, Nick Fury considered activating the station's self destruct. After the Living Laser was defeated and remanded to a special prison cell inside the Helicarrier, Fury told Iron Man that he was a loose cannon in S.H.I.E.L.D.'s eyes and if he messed up, S.H.I.E.L.D. would apprehend him.
When the Helicarrier's engines were failing, S.H.I.E.L.D. sent for Tony Stark so that he could repair the Helicarrier's engines. Stark ended up in an argument with Nick Fury when he learned that the Living Laser was dying. There, Tony also learned that his father made weapons for S.H.I.E.L.D.
S.H.I.E.L.D. reappeared when Tony Stark offered to help the Living Laser. The Ghost sprung the Living Laser from the Helicarrier and disabled the engines as a distraction. Tony managed to get the engines back on-line and save the Helicarrier. Later, Tony as Iron Man led the Helicarrier to A.I.M. headquarters where S.H.I.E.L.D. agents searched the entire compound.
The Black Widow under the employ of Justin Hammer stole top secret data for an adamantium/vibranium alloy and a sample from the Helicarrier. Nick Fury reluctantly asked Iron Man for help getting it back, but after seeing S.H.I.E.L.D.'s new Mandroids robots, which were made from Iron Man's armor tech, he blew them off. S.H.I.E.L.D. detected the stolen sample's radiation signature on Iron Man's suit. Thinking he was the thief, Fury prepared the Mandroids to capture Iron Man. He eventually defeated them and captured the Black Widow for S.H.I.E.L.D., proving his innocence, but failed to get the alloy sample and data back. Nick Fury said that he was keeping his eye on Iron Man since he destroyed government property. Fury later talked to a captured Black Widow and gave her a choice to spend years in a maximum security jail or be a special operative for S.H.I.E.L.D.
When a fired agent named Mallen stole an experimental super-soldier serum called Extremis and took it, he transformed into a mutated human and started assaulting S.H.I.E.L.D. agents. When Iron Man showed up to stop him, he mercilessly beat him down to near death. S.H.I.E.L.D. managed to drive him off and they took Iron Man to the Helicarrier for medical treatment. They managed to save his life and in doing so, found out his true identity. He was frustrated to learn that he had to retire Iron Man for his general health. When he learned about the serum and a certain frozen hero in the Helicarrier, he made another serum and injected himself with a drop of it. As a result, his heart was fixed and he gained the ability to communicate with computers and machines, even his Iron Man suit. He went back for a rematch against Mallen and used his new abilities to find an electric cable under the ground and used it to electrocute Mallen into a coma. Back at the Helicarrier, Stark offered to upgrade their security so this didn't happen again. He received thanks from Nick Fury and offered him a place on a "team" when he turned 18. Iron Man declined, saying that he was not really a team player.
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