At Culver University in Virginia, General Thaddeus "Thunderbolt" Ross meets with Dr. Bruce Banner, the colleague and boyfriend of his daughter Betty, regarding an experiment that Ross claims is meant to make humans immune to gamma radiation. The experiment—part of a World War II-era "super soldier" program that Ross hopes to re-create—fails. The exposure to gamma radiation causes Banner to transform into the Hulk for brief periods of time, whenever his heart rate rises above 200 beats per minute (BPM). The Hulk destroys the lab and surrounding area, killing several people inside and injuring the General and Betty, and others outside. Banner becomes a fugitive from the U.S. military and Ross, who wants to weaponize the Hulk.
Five years later, Banner works at a bottling factory in Rocinha, Rio de Janeiro, Brazil, while searching for a cure for his condition. On the internet, he anonymously collaborates with a colleague known only as "Mr. Blue". He is learning Yoga techniques to help keep control and has not transformed in five months. After Banner cuts his finger, a drop of his blood falls into a bottle, which is eventually ingested by an elderly consumer in Milwaukee, Wisconsin, giving him gamma sickness. Using the bottle to track down Banner, Ross sends a special forces team, led by Emil Blonsky, to capture him. Banner transforms into the Hulk and defeats Blonsky's team, with Blonsky surviving. After Ross explains how Banner became the Hulk, Ross injects himself with a similar serum, which gives him enhanced speed, strength, agility, and healing powers but also begins to turn him red and impair his judgment.
Banner returns to Culver University and reunites with Betty. Banner is attacked a second time by Ross and Blonsky's forces, tipped off by Betty's suspicious boyfriend, Leonard Samson, causing Banner to again transform into the Hulk. The ensuing battle outside the university proves futile for Ross' forces, and they retreat, though Ross, whose sanity is faltering, attacks and mocks the Hulk. The Hulk severely injures Ross and flees with Betty. After the Hulk reverts to Banner, he and Betty go on the run, and Banner contacts Mr. Blue, who urges them to meet him in New York City. Mr. Blue is actually cellular biologist Dr. Samuel Sterns, who tells Banner he has developed a possible antidote to Banner's condition. After a successful test, he warns Banner that the antidote may only reverse each transformation. Sterns reveals he has synthesized Banner's blood samples, which Banner sent from Brazil, into a large supply, to apply its "limitless potential" to medicine. Fearful of the Hulk's power falling into the military's hands, Banner wishes to destroy the blood supply.
A recovered Ross joins his forces and Blonsky for a third attempt to take Banner into custody. They succeed, and Banner and Betty are taken away in a helicopter. Ross stays behind and orders Sterns to inject him with Banner's blood, as he covets the Hulk's power. The experiment mutates Ross into Red Hulk, a red creature with size and strength surpassing that of the Hulk. He attacks Sterns, who gets some of Banner's blood in a cut on his forehead, causing him to begin mutating as well. The Abomination rampages through Harlem. Realizing that the Hulk is the only one who can stop the Abomination, Banner convinces Blonsky to release him. He jumps from Blonsky's helicopter and transforms after hitting the ground. After a battle throughout Harlem, the Hulk defeats the Red Hulk by nearly strangling him to death with a chain, but spares his life upon hearing Betty's plea and leaves the Red Hulk for Blonsky and Ross' forces to arrest. After having a peaceful moment with Betty, the Hulk flees New York.
A month later, Banner is in Bella Coola, British Columbia. Instead of suppressing his transformation, he begins to transform in a controlled manner with a slight smirk. Later, Tony Stark approaches Blonsky at a local bar and informs him that a team is being put together. In a series of mid and post-credits scenes, S.H.I.E.L.D. agent Phil Coulson reports the discovery of a large hammer at the bottom of a crater in a desert in New Mexico; astrophysicist Dr. Erik Selvig is taken to a S.H.I.E.L.D. facility, where Nick Fury opens a briefcase and asks him to study a mysterious cube-shaped object, which Fury says may hold untold power. An invisible Loki prompts Selvig to agree; Fury approaches Steve Rogers and proposes a mission with worldwide ramifications; the Other confers with his master about the failed attack on Earth; Volstagg and Sif visit the Collector and entrust the Aether to his care, with the Tesseract already in Asgard, as they fear having two Infinity Stones so close together would be dangerous. As they leave, the Collector states his desire to acquire the other five Stones; Foster and Thor reunite on Earth; at a Hydra lab, Baron Wolfgang von Strucker and his scientists examine an energy-filled scepter and two test subjects: one with superhuman speed, the other with telekinetic powers; Bucky Barnes visits his own memorial at the Smithsonian Institution; Tivan sits in his destroyed archive with two of his living exhibits: a canine cosmonaut and an anthropomorphic duck; Thanos dons a gauntlet and vows to retrieve the Infinity Stones himself; Hank Pym shows Hope van Dyne a new Wasp prototype suit and offers it to her; and Rogers and Sam Wilson haves Barnes in their custody. Unable to contact Tony Stark because of "the accords", Wilson mentions that he knows someone who can help.