The newly reformed Levi Squad, now composed of Eren and his six remaining cadet friends, are camped out in a remote cottage where Hange carries out experiments on Eren to test his Titan abilities. Hange reports that Pastor Nick has been tortured and murdered in the Trost District barracks but she accuses the Military Police's First Interior Squad of being responsible. Levi suspects that someone in the government has their sights set on destroying the Survey Corps and concealing the secrets of the Titans. After Nifa delivers a message from Erwin, who has been arrested by the Military Police, Levi has the Scouts abandon their hideout only shortly before the Military Police arrives to raid it. Levi figures that the government is after Eren and Historia, and he decides to head back to the Trost District. Before Hange leaves with Moblit to go after Erwin, Eren gives her a written copy of the conversation he recalled between Ymir and Bertholdt. The Scouts arrive secretly back in Trost, and Jean and Armin - disguised as decoys for Eren and Historia - are soon abducted by Dimo Reeves, who was hired by the Interior Police, but Mikasa and the others easily rescue them and capture their kidnappers. Meanwhile, Levi shadows Eren and Historia's transport from rooftops with Nifa and two other soldiers from Hange's Fourth Squad. He instinctively feels uneasy and tells Nifa about Kenny the Ripper, a notorious serial killer he knew in the past, when suddenly Kenny and his henchmen appear and ambush them with slug guns, killing Nifa and the rest of her team before confronting Levi.

Kenny, now working for the First Interior Squad, pursues Levi with members of his Anti-Personnel Control Squad. Kenny finds Levi hiding in a tavern, but Levi escapes after shooting Kenny with the bar owner's musket and killing several of Kenny's men. Nearby, Mikasa and the other scouts hear the commotion and are forced to defend Historia and Eren's wagon, which involves killing human attackers, something they have never done before. Armin is traumatised after his first ever kill is Jean's female attacker when she faltered. However, the Interior Police attackers overwhelm them and kidnap Historia and Eren with tranquilizer darts. In the capital city Mitras, the Royal Government receives a message from Lord Rod Reiss that Historia and Eren have been captured. Following their savage battle with Kenny's group, Armin and the others are traumatized from having to kill other humans, after which Levi consoles them. They interrogate Dimo Reeves, who was coerced into helping the Military Police but now fears for the future of his company and the people in Trost, so Levi offers him protection for the people of Trost in exchange for his help. Elsewhere, Hange approaches Erwin to help, suggesting that Eren will be eaten if they do not rescue him. With Reeves' assistance, the scouts capture some Interior Squad soldiers Djel Sannes and Ralph, who murdered Pastor Nick, and torture them about the whereabouts of Historia and Eren. They discover Historia is the real heir to the throne and conclude she is being held by her father, Rod Reiss. Later, Reeves is killed by Kenny for betraying him, unaware that Reeves' son, Flegel, witnessed it when hiding in the shadow.

In a flashback, Historia tells the Scouts of her upbringing on the Reiss estate inside Wall Rose, her estrangement from her mother, Kenny's execution of her mother and her being forced to adopt the identity of Krista Lenz. In the present, Rod heads back to his family estate with Historia and Eren while Hange explains to the Scouts that Eren will be eaten to acquire his Titan powers and abilities. Meanwhile, Erwin explains to Commander Pyxis his plans of a bloodless coup d'état to overthrow the corrupt Royal Government, so Wall Maria can be retaken. Erwin gains Pyxis' support after telling him that Sannes confessed that the current king is a fraud, and the Scouts plan to have Historia enthroned as Queen. He also reveals that his father was murdered after telling Erwin that he believed the real reason for the fighting within the walls was to protect the land and property of the wealthy, not humanity. To insulate the other Scouts, Erwin then surrenders to the Military Police who frame him for the murder of Reeves after he appoints Hange as his successor. Outside the city, Squad Levi split up and head for the Reiss estate to prepare for their rescue mission of Historia and Eren, but they are being tracked by the Military Police.

Squad Levi captures the two soldiers tracking them, who happen to be Marlowe and Hitch, Annie's friends in the Military Police. After learning the truth that Annie was the Female Titan and the Scouts are being framed, Marlowe and Hitch agree to help them by telling them of an outpost that is the least guarded by the Military Police. Squad Levi subdue the soldiers at the outpost while Levi tortures the Interior Police officer in charge for Eren and Historia's location. Meanwhile, Hange rescues Flegel from the Military Police, who are trying to kill him to cover the truth that his father was killed by the Interior Police. With Hange and Moblit's help, Flegel lures the Military Police to the Stohess District and tricks them into confessing the truth about his father's death and the government trying to frame the Scouts and cover up the truth in front of the residents of Stohess and some reporters before capturing them. With the people no longer fooled by the government's propaganda, Hange begins her next plan. Elsewhere, as Erwin is brought before the King to be sentenced for execution, he warns his friend Nile he must choose a side before Pyxis begins the coup.

At his trial before the fake king and the royal council, Erwin unsuccessfully puts his case to reclaim Wall Maria and avoid a potential civil war caused by people competing for limited resources. Just as Erwin is sentenced to death, news arrives that Wall Rose has been breached by Titans. However, rather than allow Wall Rose refugees shelter within Wall Sina, the council orders the gates closed, sacrificing the entire Wall Rose population. A disgusted Nile refuses to obey the order, and Chancellor Darius Zackly arrives with his troops, revealing the news of the breach was a ruse. With the council's self-interest and disregard for human life now revealed, Pyxis announces the Military will take over the government and publish the news in the press. Later, the remaining scouts receive the news, and Hange tells the others about the mysterious deaths of Rod Reiss' family at their Chapel. Meanwhile, in a crystalline cavern, a chain-bound Eren is approached by Historia.

Historia assures Eren that her father has good intentions even though he created problems for the Scouts and killed Pastor Nick. Rod then instructs Historia to touch Eren, triggering subconscious memories which leave Eren traumatized from learning that he was turned into a Titan by his father Grisha and ate his father on the night he received the basement key. The process also unintentionally triggers Historia's memories of a young woman named Frieda, whom Rod reveals to be Historia's half-sister, who erased herself from Historia's memories. Rod explains that Frieda possessed the Founding Titan power inherited in their family, before Grisha, who was also a Titan Shifter, devoured her for it while slaughtering her four siblings and mother. Later, Kenny arrives and updates them on the coup before preparing to defend the crystalline cavern beneath the Reiss chapel with his men. Meanwhile in the capital, Pyxis reveals to Erwin that the Reiss family possess the power to alter people's memories, and Erwin leads a force out to rescue Eren. As Kenny Ackerman prepares his defense, he recalls his grandfather saying that the Ackermans were once bodyguards to the Reiss royal family but were exiled as the Reiss memory altering powers had no effect on them. Meanwhile, Squad Levi finds a hidden trapdoor in the floor of the Reiss chapel, and they prepare to descend and rescue Eren.

Squad Levi storm into the cavern and engage Kenny and his Anti-Personnel Control Squad, forcing the enemy to retreat back into their final defensive position. Meanwhile, Rod explains to Historia that the cavern and city walls were built a century ago by their ancestor, who used the Founding Titan's power to erase the memories of all citizens except a few immune bloodlines. Generations later, Frieda inherited the Founding Titan and the memories of their world before the walls. Rod explains that Frieda metaphysically lives on within the Founding Titan, with Historia realizing that she must become a Titan and eat Eren to gain the Founding Titan and see her sister again. When Kenny arrives and overhears that only those of the Reiss bloodline can use the Founding Titan's power, he furiously confronts Rod and decides to wound Eren so Historia will have to fight Eren to acquire the power. Historia is about to inject herself with the Titan serum when she sees Eren is too guilt-ridden to resist. She then remembers Ymir's wish for her to live a prideful life, and realizes that Rod's true intent is restoring his family's power, and the will of her ancestors to preserve the status quo will consume her like it did with Frieda and those before her. Historia then angrily refuses to proceed, breaking the syringe and slamming her father into the ground breaking his back, before grabbing the keys to free Eren. Desperate, Rod licks up some of the serum from the broken syringe on the ground and transforms into a massive Titan.

Squad Levi break into the cavern and help Historia free Eren before being cornered by the Titan Rod Reiss, whose gigantic size causes the cavern to collapse. While Kenny and his squad is being crushed by falling boulders, Eren drinks a serum that allows his Titan form to harden and prevent the ceiling from falling, saving his friends. The Scouts retrieve Eren from his crystallized Titan body and head back towards the Orvud District at Wall Sina. Meanwhile, Rod's Titan crawls towards Wall Sina with no one able to get close without being incinerated by body heat that is burning everything in his path. After some discussion over how to handle the situation, everyone agrees that Rod must be killed. Returning to the Orvud District, Levi reminds Historia that since she has royal blood, she must become the queen to complete the transition from the old government, to which she reluctantly agrees on the condition to help in the battle against Rod's Titan. As Rod's Titan approaches, Erwin surprisingly decides not to evacuate the citizens of Orvud.

Erwin justifies his decision to not evacuate Orvud District because Titans are attracted to the density of human populations, so they can use this to their advantage by luring Rod's Titan into a trap. Erwin's plan works initially, as they manage to get Rod's titan close to the wall where the trap is set. However, the Garrison Corp's cannon barrages have little effect, and Rod's Titan eventually reaches and towers against the wall. As its face and chest have eroded from crawling for miles on the ground, the Scouts then implement their own plan. They first ram the Titan's supporting arms with gunpowder-loaded carts and destroy them with the ensuing explosion. After the Titan falls face-first onto the top of the wall, Eren assumes his Titan form and plunges a bundle of gunpowder barrels into its gaping mouth. After the Titan's nape is blown from within, the Scouts then quickly mop up the airborne fragments with their 3D Maneuver gears. Historia succeeds in destroying the main fragments holding Rod, killing her father and seeing some of his memories, before falling into a cushioned wagon below in the city street in front of astonished residents. She recovers from her fall and formally introduces herself to the gathered civilians as the true ruler of the walls. Back at the Reiss estate, a mortally wounded Kenny recalls events in his past before being found by Levi.

As he lies dying, Kenny Ackerman recalls his past: his capture many years earlier by Uri Reiss in his Titan form; pledging loyalty to the family after Uri begged his forgiveness for the Ackerman family's persecution; bringing up his dead sister Kuchel's son Levi and teaching him the ways of a killer; becoming leader of the clandestine Anti-Personnel Control Squad; and wondering if the Reiss family's power could grant him the luxury of being compassionate. Kenny then explains to Levi why he has not injected himself with the Titan serum he stole from Rod Reiss' bag and Levi presses Kenny to reveal what he knows about Titans and his own family. With his dying words, Kenny reveals himself as Levi's uncle before handing him the package containing the Titan serum. In the capital, Historia is crowned queen with Levi congratulating her while thanking the Scouts for their effort in killing the Rod Reiss Titan. Meanwhile, the Beast Titan defeats Reiner and tells him and Bertholdt that they will locate the Coordinate as their next objective, overruling the pair's desire to find and rescue Annie Leonhart.

Two months after Historia's coronation, the military have purged remaining traces of the old regime. They also gained an abundant supply of crystals from the Reiss estate. Meanwhile, Eren perfects his Titan hardening ability and Hange develops a new guillotine weapon nicknamed the "Executioner from Hell" that allows defenders to easily kill Titans without loss of human life. Eren realizes that Training Corps commander Keith Shadis was the man who knew his father Grisha in his memories, and the Scouts visit him. Keith tells them that he met Grisha, who claimed to have suffering from amnesia, almost twenty years ago outside Wall Maria. Grisha learned about life within the walls, offered to work as a doctor, and later married Carla. During the Fall of Shiganshina, after learning about his wife's death, Grisha took Eren into the woods where Keith later found the boy alone wearing a key around his neck. Keith resigned as Commander of the Survey Corps out of the guilt of losing his men because Grisha praised him of being "special" and he believed it. After hearing his story, Eren claims he is merely the son of a special man, and the Scouts make preparations to retake Wall Maria.

Hange is unable to analyse the Titan Serum's formula because of its volatile nature so Erwin entrusts it to Levi in the event it must be used to turn someone into a Titan. Erwin confirms arrangements are in place to retake Wall Maria, then he reveals a secret plan to use the Scouts to search the Yaeger family's basement. After the rest of the lieutenants leave, Levi tries to convince Erwin to remain behind and let Hange command the Scouts, but Erwin insists on leading the operation. On the night before their mission, the Scouts are treated to meat for dinner. Tensions are high, leading to a fight over portions and Eren provokes a fight with Jean. Later, Eren, Mikasa and Armin reminisce over their past, and reflect on their hopes for a future of life beyond the walls. On the day of the expedition to retake Wall Maria, the people of Trost gather to cheer on the Scouts and wish them success. As the Scouts ride out, Bertholdt and Reiner stand guard on Wall Maria.

In a mid-credits scene, Levi berates a shocked Eren and Mikasa, while standing beside two apparent corpses. He smashes Eren across the face, which causes Mikasa to attack him and hold him at blade point.

The Survey Corps treks through the forest under the darkness of a new moon, planning to retake the Shiganshina District in order to reach Eren's basement. On the way, they see a sleeping titan but manage to pass by without waking it up. The group arrives at the seemingly empty Shiganshina District and Eren easily blocks the hole in the outer wall with his titan hardening ability. Before Eren plugs the hole in the inner wall, Armin discovers a recently abandoned campsite and is given command to search for enemies planning an ambush. Armin assigns members of the Survey Corps to search for cavities within the walls and before long, Reiner bursts from a disguised hole in the wall and transforms into the Armored Titan. Suddenly, the Corps find themselves surrounded by Titans and the Beast Titan seals the inner entrance with a thrown boulder, trapping the horses within Shiganshina and preventing the Corps from using them to escape.

Reiner, as the Armored Titan, initially begins climbing up the wall towards the Survey Corps when the Beast Titan gives a signal and the 2-3 meter Titans within Wall Maria rush towards the wall, targeting the horses to cut off the escape route of the Survey Corps. Three squads are sent to protect the horses, while the Levi and Hange squads prepare to tackle the Armored Titan utilizing Thunder Spears. Erwin initially keeps Levi and Armin back, to target the Beast Titan. Meanwhile, the Armored Titan reaches the top of the wall and encounters Erwin waiting for it, but suddenly Eren transforms into his Titan form and flees. The Armored Titan takes the bait, abandoning its target of the horses, and chases Eren. They engage in a battle of force and wits as each tries to gain the upper hand, but Eren's training of hardening his hands pays off as he temporarily weakens the Armored Titan. Hange and her squad then attack it with Thunder Spears, aiming for the nape of the neck. Their initial attack weakens the Titan, so they follow up with a barrage of the spears in an attempt to finally destroy the Armored Titan along with Reiner.

As Bertholdt waits in his hiding place, he thinks back to the Battle of Trost where he, Reiner, and Annie were forced to leave a defenseless Marco to be eaten by Titans after he overheard their strategy to stop Eren from plugging the hole in the wall. Bertholdt then recalls himself and Reiner meeting with the blond man in Shiganshina some time before the Survey Corps arrive, with Reiner criticizing his friend's lack of commitment. Back in the present, the Armored Titan lets out a roar, signalling the Beast Titan to throw a barrel containing Bertholdt into Shiganshina. Seeing Reiner down, hoping his friend can hear him, Bertholdt does not immediately transform and instead confronts the Scouts. Armin attempts to negotiate with him, but Bertholdt reveals to have found his resolution and intends to kill everyone before swinging himself high into the sky to transform into the Colossal Titan, creating a massive fiery explosion. With the fate of Hange and her group ambiguous, Armin hesitates over attempting an attack or retreat as the Colossal Titan begins to advance towards the inner wall.

Bertholdt's Colossal Titan turns Shiganshina into a sea of flames by scattering burning debris. Armin is frozen by indecision, handing command over to Jean as they head for the river and stay hidden. Outside the wall, the Beast Titan pitches a barrage of stones towards the scouts holding the horses, shredding buildings and causing casualties among them. Levi has the remainder regroup with Erwin at the Wall's base. Back in Shiganshina, Eren vainly tries to stop the Colossal Titan by grabbing its foot, only to be knocked unconscious when kicked onto the wall. Jean orders Armin's team to attack with Thunder Spears, but the Colossal Titan deflects them with a huge burst of steam. The situation looks hopeless before Erwin suggests a counter-attack with himself and the remaining recruits as a sacrificial diversion so Levi can kill the Beast Titan, knowing that he would likely die without ever learning the truth concealed in the basement of Eren's house. Erwin gives a rousing speech to the recruits, convincing them that it is better to die fighting than be killed while hiding from flying rocks, and leads the charge towards the Beast Titan through a hail of rocks.

Erwin is mortally wounded while leading the charge against the Beast Titan, the Beast Titan expressing mixed feelings while decimating the recruits as Levi reached him by taking out the Titans on his right flank. Levi manages to incapacitate the Beast Titan and rips the blond man out after inflicting enough injuries to keep him from resuming his Titan form, intending to turn one of the casualties into a Titan to feed the war chief to. But the Cart Titan snatches the blond man in its mouth and runs off, the man admitting he underestimated Levi while ordering the remaining Titans to attack him. Meanwhile, Armin realizes the Colossal Titan is immobile while using its steam and gives Eren some detail of his plan while the others hold off a somewhat confused Armored Titan, Reiner having lost his most recent memories due to the last attack. The group, joined by Hange who survived Bertholdt's transformation thanks to Moblit placing himself between them and the blast, use two of their remaining thunder spears to shatter the Armored Titan's jaw hinges so Mikasa can use hers to blow Reiner out of his Titan body. When Eren's Titan form seems to be suffering a concussion, Armin deliberately challenges the Colossal Titan by having his ODM gear hook into the monster's tooth. Bertholdt proceeds to burn Armin alive in his steam, learning too late that Armin used himself as a distraction so Eren can harden his Titan form and, in human form, covertly maneuver himself into position to rip Bertholdt out of the Colossal Titan. In the aftermath, Eren drags the limbless Bertholdt towards the severely burnt Armin whom Eren recalls has always been braver than perceived to be.

Eren finds himself alone with Armin's burnt body and the unconscious Bertholdt. His reverie is interrupted by the Cart Titan carrying the blond man, who asserts that Eren was lied to by his father. The blond man departs when Levi arrives, still in pursuit, promising to return and save Eren. Meanwhile, after Hange takes a letter from Ymir which Reiner had, Hange tries to kill him before being convinced by Jean to have Mikasa fetch the Titan serum from Levi so they can transfer the Armored Titan power to one of their own. But the Cart Titan rescues Reiner, and Mikasa finds out that Armin is severely injured but still alive as Levi prepares to inject him with the serum. At that moment, Floch Forster, the only surviving recruit from the suicide charge, arrives with the mortally wounded Erwin. This causes Levi to consider Erwin instead, causing Eren and Mikasa to openly defy that decision with the latter attacking Levi until being restrained by Hange. Once everyone calms down, Levi orders everyone to leave and prepares to inject Erwin. But Erwin withdraws his arm in delirium, causing Levi to recall his conversation with Erwin before the suicide charge and ultimately chooses to let the commander rest in peace and give the serum to Armin instead. As Erwin succumbs, Armin becomes a mindless Titan and eats Bertholdt. Levi and Hange mourn the deceased Erwin while the rest of the squad share an emotional moment as Armin emerges healed from his Titan form.

Armin has a nightmare of a weeping Colossal Titan, waking up with no memory of the events following Bertholdt's transformation. The nine remaining members of the Survey Corps huddle around him to explain their situation, Armin struggling to come to terms with Levi's decision to save him instead of Erwin. Hange, Levi, Eren and Mikasa return to Shiganshina to investigate the basement of what remained of Eren’s home. Levi kicks open the basement door when Grisha's key cannot unlock it, the group learning that it actually opens a desk drawer with a hidden compartment containing three well-preserved books. The group finds one book holding a picture of Grisha, standing next to a woman holding an infant child who are neither Karla or Eren. An inscription written by Grisha on the back explains the picture to be a photograph created by technology from a land beyond the walls, where people live in luxury. As what remained of the Survey Corps return to the city, Nile Dok confides to the council that Erwin once considered the possibility that there may be humans living beyond the walls.

In a post-credits scene, Eren begins reading Grisha's book which opens with Grisha recounting a time in his youth when he and his sister, Faye Yeager, lived in a city beyond Mitras and Wall Maria, the world Eren knows today. The children watched an airship fly overhead, and against their mother's instructions, Grisha impulsively dragged Faye beyond the walls of their district to watch it land.

While Eren and Mikasa were held in the stockade after their actions in the aftermath of the Battle of Shiganshina, Eren has a dream of experiencing the life of his father Grisha starting when he took his younger sister Faye outside the Liberio Internment Zone for Eldians to watch the zeppelins. However, they are caught by two Public Safety soldiers. Not wanting to trouble his parents, Grisha took a beating for himself and Faye by Kruger while his partner Gross offers to take Faye home. But Faye's bloodied corpse is found the next day with Grisha knowing Gross murdered his sister. Gross lies to Faye's parents, claiming he took her back to the Liberio Internment Zone. Faye's father tells Grisha their people's history and the Marley nation's justifiable prejudice towards them, accepting the officer's lie. In his adult years, Grisha joins the Eldian Restoration movement after learning the truth of Faye's death from an Eldian named Grice. The movement is supported by the secret informant "Owl", Grisha learns the Eldians' true history while eventually marrying Dina Fritz, the last remaining Eldian with royal blood on the mainland, and they have a son, Zeke, who appears with them in a photograph. When Marley begins its Warrior program to keep up with rival nations over natural resources, Grisha's attempt to raise Zeke as an infiltrator backfires, as his son becomes loyal enough to turn the Restorationists over to the authorities, including his own parents. Grisha and his fellow Restorationists are then taken by boat to the perimeter wall of Paradis Island for exile as mindless Pure Titans once injected with Titan spinal fluid. Grisha recognizes Kruger and Gross among the squad as Gross kicks Grice off the wall and gives him a head start before turning the others into Titans, including Dina who ironically becomes the Titan that will eventually devour Eren's mother. Gross admits to killing Faye and was about to kick Grisha over the wall, only to be suddenly shoved by Kruger and eaten by a Titan. Kruger reveals himself to be both the Owl and a Titan shifter as he transforms into the Attack Titan and annihilates the rest of the Public Safety soldiers.

Armin transcribes Eren detailing Grisha learning the Owl's full name as Eren Kruger, the officer explaining how his desire to restore Eldia led to him participating in his people's persecution to maintain his cover. Kruger then reveals that those who possess the Titan Power live for only thirteen years, along with the two means of succession and the nature of the Coordinate, requesting Grisha to infiltrate Paradis and take the Founding Titan from the royal family. Kruger explains his reasons of selecting Grisha while advising him to start a new family before proceeding to inject him with the Titan serum, mentioning Armin and Mikasa to his own amazement. In the present, Eren and Mikasa are released from the stockade to participate in the conference among the government. Historia also attends after reading Ymir's farewell letter, glimpsing in her friend's memories as a result. With the evidence presented before the council, Hange expresses regret that their enemies now include other humans in addition to Titans while stating Eren could command the Pure Titans despite not being of the royal bloodline. It was then that Eren realizes that he commanded the Pure Titans because he touched Dina's Pure Titan form, keeping it to himself out of fear of what the military might do to Historia if he revealed this knowledge.

At the meeting of the Paradis government, Historia decides the people within the walls must be told the truth about the Titans which had been kept secret for 100 years and that the breaching of the wall by Titans was the beginning of a planned invasion by the state of Marley. This information is met with mixed reactions among the population. When Hitch approaches the survivors at a ceremony to honor their fallen comrades, Floch tells her what a hero Marlo was. He also raises the difficult question of why Armin was given the serum instead of Erwin, a controversial decision even among the survivors. As Historia presents the nine survivors with their medals, Eren touches her hand, and immediately he is flooded by memories of the Fritz royal family, indicating a connection through Titan blood. Within a year after the attack on Trost District, the Titans inside Wall Maria have been killed and the inhabitants return to their hometowns to begin rebuilding and farming. Six years after the fall of Wall Maria, the Survey Corps including the survivors again begin expeditions outside the wall. One day they find a Titan unable to move because of its small arms and legs and realize that they must be close to the perimeter wall where Eldians are turned into Titans by Marley. Riding further on, they finally arrive at the wall where Grisha became a Titan, and for the first time they see the shimmering ocean. They joyfully play in the water, though Eren realizes that they only found enemies across the sea instead of the freedom he has been seeking. He then points out into the distance and wonders if they kill all their enemies over there, would they finally be free.