Hawkeye, with the permission of Nick Fury, tested the security of the Helicarrier in a faux hostile insertion. He was able to infiltrate the ship and get through many of its checkpoints. He advised Fury of the ship's flaws that he was able to exploit.
In the Destruction of Project P.E.G.A.S.U.S., Loki had returned to Earth to conquer it. After destroying the Joint Dark Energy Mission Facility and stealing the Tesseract, Loki traveled to Stuttgart, Germany to steal Iridium. Captain America and Black Widow traveled to Stuttgart in a Quinjet to confront him. Loki gets the upper hand on Rogers until Iron Man arrives and Loki surrenders. They take Loki into S.H.I.E.L.D. custody aboard the Helicarrier, where he was placed in a confinement capsule designed to hold the Hulk. Loki taunted Nick Fury about his attempts to control the Tesseract and his gathering of misfits to defend Earth.
Loki's mere presence was enough to provide a disruptive element that would fragment the only group of heroes that had any hope of stopping him.
When Black Widow arrived to speak with Loki, apparently to offer a deal in exchange for Hawkeye's freedom, he subjected her to a play of wits where he ferreted out her deeper misgivings, but was completely caught off-guard when she tricked him into revealing that there was already a monster among them on the carrier. From this, she concluded that the monster was Bruce Banner and that he had planned to use the Hulk to destroy the ship and the heroes as well.
However, Loki's plan to use the Hulk was only one aspect of his real intentions. Unbeknownst to S.H.I.E.L.D., another Quinjet carrying Barton and the rogue agents came to his aide, following a signal transmitting from the Scepter. Barton uses an explosive arrow to destroy one of the rotors and lands on the Helicarrier. The explosion knocks Romanoff and Banner to a lower level, where the wounded Banner transformed into the Hulk. Banner chases Romanoff until Thor intervenes and begins fighting Banner.
Barton and the mercenary team head to the bridge where S.H.I.E.L.D. agents led by Nick Fury and Maria Hill engage them. The mercenaries are killed but Barton uses a special arrow to hack the computers and sabotage a second rotor. Fury orders an F-35 Lightning II to fire on Banner while he was engaging Thor. The attack is futile, as it only angers Banner, who jumps on the jet and tears it apart. Banner plummets to the ground below and crashes through the roof of a large building, after the pilot manages to eject and parachute to safety.
While everyone else was fighting the perpetrators, Iron Man and Captain America fixed the rotor that the attackers destroyed. After getting the rotor moving, Stark got trapped inside until Rogers defeated two mercenaries and pulled the lever to slow the rotor, saving Stark from being shredded. Romanoff intercepts Barton on his way back to the Quinjet. The two fight for a while until Romanoff hits Barton in the head hard enough to break his brainwashing.
Loki then used illusions of himself to trick Thor into entering the cell. Agent Phil Coulson arrives but Loki uses another illusion to fool him and stabs Coulson in the back with the Scepter and ejected Thor's cell from the Helicarrier. Before Loki can leave Coulson shoots him with the Destroyer Armor Prototype Gun. Loki escaped on the Quinjet while Fury and the medics get to Coulson, but it was too late. Thor used Mjølnir to break the glass and escape the cell before it collided with the ground.
Enraged by Phil Coulson's death, the Avengers decided to end the war Loki had started by defeating him in the Battle of New York. It turned out that Coulson was dead for days, but Nick Fury had S.H.I.E.L.D.'s scientists working their hardest to save him with Project T.A.H.I.T.I.
After both the attack and the Battle of New York, Tony Stark designed new repulsor technology for S.H.I.E.L.D.'s new Helicarriers for their Project Insight, in order to avoid what happened during the attack.