One hundred years ago, the Titans suddenly appeared and decimated most of humanity. To stop their advance, humanity built walls and lived peacefully there for another 100 years. In the present day, Eren Yeager expresses to his friends, Armin Arlert and Mikasa Ackerman, his desire to leave the Walls and see the outside world. After a failed attempt to leave the walls, Souda, the captain of the Garrison, explains to them that the military is assembling a scouting regiment to explore beyond the walls. However, the Wall is suddenly attacked by the Colossal Titan, who causes a hole in the wall which leads the Titans to enter and rampage. Unable to find Mikasa, Eren assumes she died during the attack.

Two years later, Eren and Armin enter the Scouting Regiment, along with Sasha Braus, Jean Kirstein, and others. The team, led by Military Police Commander: Kubal, move out into one of the towns of the Outer Wall. The group is then attacked by Titans but are saved by Captain Shikishima and Mikasa, who survived the attack from two years ago. Eren eventually confronts Mikasa and she reveals to him that the experience made her realize the world is cruel. After realizing that Mikasa and Shikishima are most likely together, Eren is once again devastated. The group is attacked once again. Jean attempts to convince Eren to flee but Eren chooses to fight back before losing his leg in the process. Eren manages to save Armin from being eaten but at the cost of his own life. Though crushed by Eren's death, Mikasa keeps fighting until she loses gas and comes face to face with the same Titan that ate Eren. However, a Rogue Titan emerges from within it and begins battling the other Titans. Souda and Mikasa realize that the Titan is Eren and free him before he is absorbed.

Eren is captured up by Kubal and his squadron, believing he is a threat to humanity. Armin tries to convince Kubal of Eren's innocence but is ignored. Before Eren is executed, another intelligent Titan appears, killing Kubal and his squadron before fleeing with Eren. Eren awakens in a mysterious bunker with Shikishima, who reveals the origins of the Titans and his plans to launch a coup against the corrupted government, which Eren agrees to help with. Eren, Shikishima, and his troops reunite with Mikasa and the others. Shikishima attempts to recruit them into his coup but when the true sinister purpose behind his plan is revealed, Eren backs out. The remaining regiment neutralize Shikishima's troops and Shikishima reveals himself to be the Titan that took Eren earlier. Eren transforms into his Titan form and battles the Shikishima Titan, with Eren emerging victorious in the end. Titan Eren proceeds to climb the wall and plants a bomb to create a massive blockage to prevent more Titans from entering.

Having survived the earlier attack, Kubal attempts to stop the group but is shot by Sasha, forcing him to transform into the Colossal Titan. As Eren, Jean, and Mikasa battle the Colossal Titan, Shikishima reappears in his Titan form and lodges the bomb into the Colossal Titan's mouth, killing them both. The detonation successfully closes the hole in the wall and Eren and Mikasa stand at the top of the wall overlooking the ocean.

In a post-credits scene, footage of the battle with the Colossal Titan is analyzed, in Shikishima's bunker, by an off-screen character, who says that Eren and Mikasa's methods are what makes them "interesting".