Following the Battle of New York, Alexander Pierce and several HYDRA operatives under the guise of S.H.I.E.L.D. agents headed to the Stark tower. While Jasper Sitwell and the S.T.R.I.K.E. team retrieved Loki's scepter to be studied by List, Pierce ordered the Avengers that Loki and the Tesseract be relinquished to them, especially the latter one since it has been S.H.I.E.L.D.'s property for 70 years.
This ensues a heated argument with Thor, who felt necessary to return the Tesseract to Asgard as Loki because he had to be punished by Odin for his crimes on Earth. However, Pierce's attempts to retrieve them ended in naught, as Thor succeeded in retaining custody of both Loki and the Tesseract, and returned them to Asgard along with himself.
Alexander Pierce is a high ranking HYDRA member who has infiltrated the World Security Council. Before the events of the film, during a mission in Bogota, Pierce met SHIELD agent Nick Fury, who saved several lives including his daughter. Surprised by Fury's actions, Pierce went on to appoint Fury as the director of SHIELD.
Several years later, the HYDRA influence over SHIELD has increased, and a trio of Helicarriers are built under 'Project Insight.' They were meant to form a SHIELD security network to protect the world. But secretly, HYDRA wanted to use them to kill and target over 20 million people that were selected by HYDRA scientist Arnim Zola's algorithm, which means that any individual that posed a threat for HYDRA would be irrelevant to HYDRA's new world order.
After his discovery of a SHIELD arsenal by Georges Batroc, which was really planned by Fury, Pierce initiated the Winter Soldier to assassinate him. But after an attack by the Winter Soldier, Fury retreated to Steve Rogers' apartment and tells him not to trust anyone because he realizes that SHIELD has been compromised before (seemingly) being fatally shot by the Winter Soldier.
Following the apparent death of Fury, Pierce meets with Rogers and thinks that he has hidden something. Pierce afterward sends agent Brock Rumlow and his team to capture Rogers, who rendezvous with Black Widow for help. He assigns the Winter Soldier a new objective to assassinate Captain America and Romanoff, although he was ultimately forced to shoot his housekeeper when she stumbled upon his meeting with the latter. After an investigation on HYDRA sleeper agent Jasper Sitwell for the real point behind 'Project Insight', Captain America, Black Widow, and their ally Falcon get captured by SHIELD, but it turns out they get rescued.
Proceeding with his plot, Pierce meets with the World Security Council members to activate 'Project Insight'. But unknown to him, Rogers and his team infiltrate the Triskelion and they reveal HYDRA's true motives motivating every good SHIELD agent to stand up against Pierce, Rumlow, and his STRIKE team. As Captain America and Falcon infiltrate the Helicarriers, they change the targets according to Zola's algorithm and turn the Helicarriers into the targets. While this goes on, Black Widow rescues the hostage World Council members and forces Pierce to help her and the seemingly alive Nick Fury to unlock every SHIELD/HYDRA secret and upload them all to the Internet.
After the destruction of the Helicarriers and HYDRA's secrets are released on the Internet, Pierce uses a small remote-controlled incendiary device to kill the other council members and threaten Black Widow, which was his way of forcing Fury to let him flee. But Black Widow disables the explosive, which gives Fury the opportunity to shoot him dead. Pierce's dying words are "Hail HYDRA."
A younger Pierce makes an appearance in the show during a flashback to 1989. During this year, Pierce sent two agents to release Werner Reinhardt, a former member of HYDRA that was sentenced to life imprisonment by Agent Carter.
Pierce appears in Endgame when Tony Stark, Steve Rogers, Bruce Banner, and Scott Lang travel back to New York in 2012 to retrieve the Space, Time, and Mind Stones. Again like the original timeline, Pierce and the HYDRA operatives posing as S.H.I.E.L.D. agents head to the Stark tower after the Battle of New York. While Rogers succeeds in obtaining the Mind Stone from Sitwell and the S.T.R.I.K.E. team, Pierce demands the Avengers that Loki and the Tessearct be handed over to them. The 2012 versions of Stark and Thor argue with Pierce, with Thor insisting that Loki, as an Asgardian war criminal, must be served justice on Asgard and punished by Odin.
Pierce ignores Thor and orders Stark to handle Loki and the Tesseract. As he and Stark fight for possession of the briefcase containing the Stone, Lang creates a diversion by causing Stark's past self to fall into cardiac arrest after deactivating his Arc Reactor. Pierce and the others tend to the dying Stark requesting medical attention, allowing 2023 Stark to take the briefcase, only to be inadvertently knocked aside by 2012 Hulk and for the Space Stone to slide right into Loki's feet. He immediately picks it up and teleports away, leaving Pierce and the surrounding onlookers shocked that he had suddenly vanished and escaped S.H.I.E.L.D. confinement.
Trivia
In the comics, Pierce is a much younger field agent. Robert Redford let slip that he accepted the role because he wanted to portray a villain; it turns out the movie version of Alexander Pierce is a combination of the Alexander Pierce from the comics and Aleksander Lukin, the man responsible for the creation of the Winter Soldier.[1]
In an interview with USA Today, Samuel L. Jackson revealed that Alexander Pierce is a member of the World Security Council, but was not present during The Avengers.
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