The government is opposing the Scout Regiment, demanding custody of Eren and Historia. Levi runs a decoy strategy so Jean and Armin are abducted instead of the targets. Mikasa subdues the kidnappers as Levi watches Eren's hearse. While looking on, Levi is ambushed by an old adversary and his team.

Afterwards, Levi convinces Dimo Reeves to work for the Scout Regiment. Reeves lures twoInterior Squad members into a trap set by Levi's squad, and they reveal under interrogation that the Reiss family is the true royal family. Kenny kills Dimo Reeves for his betrayal, while Rod Reiss reunites with his daughter, Historia.

Meanwhile, Erwin meets Pyxis and discusses the overthrow of the government. When Hange arrives, she informs Erwin about Historia's royal lineage, and he tells Pyxis his plan to expose the puppet government and install Historia as the new queen. As dawn breaks, Erwin is called outside by the First Interior Squad to account for the murder of Dimo Reeves. He names Hange as his successor before he leaves and shortly thereafter, he and the Scout Regiment are placed under arrest.

In Capital Mitras, Gerald interrogates Erwin Smith, but does not learn what the Scout Regiment knows. Nile Dawk arrives to tell Erwin about his audience with the King, and how they will announce his sentence then. Erwin warns him that he left something up to Dot Pyxis and when it happens, it will be up to Nile and 'them' to decide.

Before Erwin can be taken away, Anka Rheinberger announces that Wall Rose has been breached, forcing the nobles to confront the scenario Erwin just spoke of. Though Dot Pyxis calls for an evacuation of the civilians in Wall Rose, the nobles override his order and demand that the gates to Wall Sina be closed. Nile Dawk refuses, and Premier Dhalis Zachary arrives in time to agree. With all branches of the military turned against the Royal Government, they enact a coup d'état and the nobility is arrested. Despite their success though, Erwin expresses misgivings about the new path humanity has taken.

Eren Jaeger learns the history of how he obtained his Titan and how five years ago his father, Grisha Jaeger, slaughtered most of the Reiss family in order to obtain their power, which was held by Frieda Reiss, the elder half-sister of Historia Reiss.

Meanwhile, the military learns that certain bloodlines are immune to the 'Scream' that can alter humanity's memories and that if they do not rescue Eren they may soon forget their coup d'état ever happened. Squad Levi arrives at the rural chapel above the underground one where Eren is being held. They prepare to attack while the Anti-Personnel Control Squad waits for them below.

Meanwhile, Rod Reiss pressures his daughter Historia into using a syringe to transform into a Titan so she can eat Eren Jaeger and reclaim the Founding Titan his father had stolen from her sister Frieda. However, Historia realizes that inheriting the Founding Titan will not save anyone because even if her sister had the power to eradicate all the Titans, there is something about inheriting the power that prevents people from using it. She chooses to shatter the syringe and works to free Eren, but her father laps up the remaining fluid and transforms into a Titan.

Squad Levi meets up with Erwin Smith and the rest of the Scout Regiment outside. Rod's Titan is twice the size of the Colossal Titan and they cannot fight it conventionally. They rush to Orvud District where they will make a stand. While there, Levi Ackermann informs Historia that she is to become Queen after this to ensure the success of their coup d'état. She agrees, under one condition.

When the Titan reaches the Wall it plants its hands on top and pulls itself upright, scattering the Garrison, which falls back. Its face has been scraped away by the ground while it was dragging itself. The Scouts take over the Wall's defense and shoot the gunpowder-laden carts into the Titan's hands, which explode, causing it to lose its grip. The Titan slumps over the Wall and Eren charges forward in his Titan form to shove the sack of gunpowder into its gaping mouth. This causes the Titan to explode and Historia Reiss slices the chunk of Titan flesh containing the nape, thus killing her father. She lands in the city below to the shock of the nearby citizens who ask if she is the one who saved them. Historia rises and declares herself the true ruler of the Walls.

Now dying, following the collapse of the Underground Chapel, Kenny tells an inquiring Levi how he is related to his mother and why he eventually left him behind. Kenny gives Levi a syringe he stole from Rod Reiss and passes away. Elsewhere in Capital Mitras, Historia Reiss is crowned as the new Queen.

Eren, his squad, Levi, and Hange visit Keith and hear his story of how he discovered Grisha Jaeger outside of Wall Maria twenty years ago. The two became friends, and Grisha inspired Keith to think he was special. However, Keith suffered many failures, both in his personal life and as an officer, and came to realize he was not special at all. He was with Grisha the night Wall Maria fell, and carried Eren out of the woods after Grisha had taken him there. Keith hoped that Eren would avoid becoming like his father, but even though he sabotaged Eren's training gear when he was a cadet, Eren would not give up. As Eren leaves in the present day, Keith realizes he could not change anything.

The night before the operation, the Scouts have a party for all the soldiers in the mess hall where they are treated to a rare meal containing meat. This turns the soldiers rowdy. Sasha Braus needs to be restrained and Eren Jaeger gets into a fight with Jean Kirschtein. After the fight is broken up and the soldiers are told to go to bed, Eren shares his renewed optimism with Armin Arlelt and Mikasa Ackermann. The following day at sunset, the Scouts are sent off from Trost District by a cheering crowd.

Armin Arlelt discovers signs of an enemy presence and leads a group of soldiers to search for their hiding place. They uncover Reiner Braun hiding inside the Wall itself, but Levi Ackermann is unable to kill him before Reiner transforms into the Armored Titan. Outside the district, the Beast Titan appears along with a small army of Titans. It hurls a boulder into the breach in the Wall's inner gate, closing off the district's only remaining ground exit and trapping the Scout Regiment's horses on the Titan side of the Wall. This cuts off the Scout Regiment's only way of escape, forcing them to face the Titans.

The Scouts at the gate struggle against the Titans due to the losses they have suffered over recent months, but inside Shiganshina, Eren creates an opportunity for the Scouts to use their new Thunder Spear weapons against the Armored Titan. Hange Squad and Levi Squad succeed in blinding the Armored Titan and destroying its nape.

Though the Scout Regiment later manages to incapacitate Reiner by partially decapitating his human body while he is still in his Titan, he manages to roar, signaling the Beast Titan to throw the barrel containing Bertholdt into Shiganshina District. The Scouts scatter, but Bertholdt does not immediately transform into the Colossal Titan after seeing the extent of Reiner's injuries. He asks Reiner to lay on his back to protect himself and confronts the Scouts alone. Armin Arlelt tries talking Bertholdt down, but the latter refuses and admits he only agreed to talk as a way to test his own resolve and willingness to fight them. After Mikasa Ackermann fails to kill him, Bertholdt leaves and uses his omni-directional mobility gear to ascend high into the air where he transforms into the Colossal Titan.

On the other side of the Wall, the Scouts are devastated by the Beast Titan's rock bombardment, leaving Erwin Smith, Levi Ackermann, and the new recruits as the only survivors. Realizing that they are likely to die, regardless of what happens, Erwin stakes everything on a final operation. He leads all the recruits on a decoy suicide charge towards the Beast Titan, so that Levi can approach undetected and kill it.

Meanwhile, Armin Arlelt splits his squad into two teams. Most of the squad leaves to hold off the Armored Titan and succeeds, thanks to the timely reappearance of Hange Zoë. Armin wakes up Eren Jaeger who is comatose in his Titan, and relays a plan that will allow them to defeat Bertholdt Hoover's Colossal Titan. Eren falls off the Wall and pretends to be unconscious while Armin distracts Bertholdt and goads him into using up all his energy to burn him alive. When Armin finally collapses, Bertholdt moves on to deal with Eren, but discovers Eren has secretly used his hardening powers to plug the remaining hole in the Wall. Eren ambushes Bertholdt from behind with ODM gear, and cuts him out of his Titan's nape, ending the battle.

After losing Reiner Braun to the Cart Titan, Hange Zoë and the rest of Levi Squad arrive to find Eren and Mikasa Ackermann struggling with Levi for the injection, either with words or by force. Hange eventually manages to talk down Mikasa and Levi has everyone clear out so he can use the injection on Erwin. However, when Erwin begins muttering a childhood memory, Levi decides it would be kinder to let him pass on. He gives the injection to Armin who eats Bertholdt and emerges from his Pure Titan as his friends gather around.

The journals detail Grisha's life from beyond the Walls, where humanity has not perished and technology has progressed enough to allow humans to live elegant lives. He learned the truth of his own situation one day when he went out to see an airship along with his sister Fay.

As an adult, Grisha joins the Restorationists, where he meets his future wife. Dina Fritz. Together they have a son, Zeke, who they plan to make a Warrior in order to infiltrate Marley's mission to recover the Founding Titan. However, they are betrayed by Zeke and are sent to Paradis Island where they will be turned into Pure Titans. Though Dina is transformed, Grisha is saved at the last moment by Kruger, who reveals himself to be the Owl, the secretive leader of the Restorationists. Kruger tells Grisha to watch as he uses a knife to cut himself and transform into a Titan.