One hundred years ago, the Titans suddenly appeared and decimated most of humanity. To stop their advance, humanity built the Walls and peacefully lived there for another 100 years.

In the present day, Armin Arlert is sent to the Monzen district to find his friend, Eren Jaeger, who is dismissed once again from his job. Accompanying him is Eren's girlfriend, Mikasa Ackerman. They find Eren in a field standing atop a dud bomb. Eren expresses his desire to leave the Walls and see the outside world, especially after they realize that the ocean does exist. The three attempt to leave the Walls but are captured by the Garrison, who suspects them as renegades, but Souda, the captain of the Garrison, orders their release. Souda explains to them that the military is assembling a scouting regiment to explore beyond the walls and attempts to coerce Eren into joining. However, the Wall is suddenly attacked by a Colossal Titan, which tears a large hole into it; allowing the Titans entrance who then massacre the Garrison. Armin, Eren and Mikasa go their separate ways in the escape. Eren saves a woman with a baby from being trampled. However, he drops the baby and Mikasa rushes over to save it and Eren and the mother are forced into a church. Despite Eren's attempts to go back for them, he can only catch a glimpse of Mikasa and the child with the Smiling Titan right behind them before he is prevented from opening the doors. He flees the church just in time before the Titans tear it open and attack all inside. Unable to find Mikasa and assuming her death, a devastated Eren stumbles along the ruins of the Monzen district.

Two years later, Eren and Armin are reunited as they both volunteer for the Scouting Regiment, along with the farm girl Sasha Blouse, Jean Kirstein, Sannagi; a farmer with siblings waiting for him, the couple; Fukushi and Lil and the single mother, Hiana. The two also find Souda, now a drunkard who volunteered as a medic for the Regiment after losing his wife and daughter to the attack. The team, led by Military Police Commander, Kubal and Squad Leader, Hange Zoe, move out into one of the towns of the Outer Wall. After Hiana hears a child's cries, Eren accompanies her into exploring, only to find that the child they have been hearing was actually a Titan. The group is attacked by Titans and forced to run into town. However, before the Titans can eat them, they are saved by Captain Shikishima and Mikasa (whom Sannagi has told them about earlier as the "Goddess" under Shikishima's regiment), who survived the attack from two years ago. The group safely makes it to the town and rest up for the night. After Souda tells them the name of Eren's girlfriend, Jean and Sannagi realize that their Squad Leader and the girl are one and the same. Later on, Eren confronts Mikasa over what happened. Mikasa tells him that while she survived, she unfortunately bears a large scar on her left side, leading to her bitterness and apathy. After realizing that Mikasa and Shikishima are most likely together, Eren is once again devastated and comforted by Hiana.

In the middle of the night, the group is attacked, leading to Hiana's and Fukushi's deaths at the hands of the Titans. The explosives they have been protecting are stolen by a cloaked figure, and Lil throws a pot of fire into the back of the truck before overpowering the thief and driving it straight into a group of Titans in the center of the town where the truck explodes. Jean attempts to convince Eren to escape, but instead Eren uses his gear to attack the Titans under Shikishima's tutelage before losing his leg in the process. Armin is captured by a Titan, with the efforts of the group to fell it not working. However, Eren grabs him from the Titan's mouth and throws him out.

Though crushed by Eren's assumed death, Mikasa keeps fighting until she loses power on her gear and comes face to face with the same Titan that ate Eren. Before it can eat her, however, a Rogue Titan emerges and begins to combat the other Titans. The Titans retreat and the Rogue briefly grabs Mikasa before dropping her and collapsing. Souda and Mikasa realize that the Titan is Eren and Mikasa cuts Eren from the Rogue's corpse before he is lost. Hange realizes the reason why the nape is the weak spot of the Titans as Eren emerges and Shikishima watches the scene with an amused smile on his face while dramatically eating an apple.