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The special operations squad consisted of some of the most elite soldiers in the Scout Regiment, having a total kill record exceeding 200, and were capable of killing almost any Titan in their path. Due to their strong bond, they were able to synchronize with each other to coordinate their attacks without direct or verbal communication. During the 57th Expedition, their mission was to protect Eren Jaeger from Titans, and their secret objective was to lure the Female Titan into a trap. The mission failed, and all members of the Special Operations Squad, except for Eren and Levi, were killed.
After the events of the supposed breach of Wall Rose and the massacre during Eren's rescue, Levi forms this squad anew with its members being the remaining soldiers of the 104th Cadet Corps Top 10 and Armin Arlelt in order to watch over Eren and Historia Reiss.
The individual members of the Special Operations Squad are all hand-picked by Levi himself, for their ability to act quickly, and make tough decisions. After Eren's induction into the Scouts, he is placed into the Special Operations Squad to be controlled and protected by his squad mates. The squad rides out to an old Scout base where they stay to prepare for the upcoming Scouting Mission.
The squad watches over Eren during his Titan transformation experiments in the days leading up to the 57th Exterior Scouting Mission. On one occasion, Eren partially transforms into a Titan while sitting down for a drink of tea. The squad reacts violently by threatening Eren, and telling him to prove he is not mankind's enemy, all while Levi attempts to calm them down. After it becomes apparent that Eren had no ill-intent, his squad members apologize by biting their hands.
On the expedition itself, the Special Operations Squad is assigned to the most secure position in the Long-Distance Enemy Scouting Formation, located in the center rear. Their duty is primarily to protect Eren and therefore, they do not plan to engage in the rest of the operation. When it becomes clear that the formation was compromised, the Special Operations Squad rides into the nearby Forest of Giant Trees with the rest of the central column. The Female Titan emerges and gives chase to the squad, however Levi refuses to give the order to engage. When Eren considers disobeying this order, Levi tells him to make whichever decision he will regret less, convincing Eren to have faith in his comrades, and continue riding forwards. After the Female Titan is captured, Levi separates to see to his own task, and the other squad members are on standby in the trees.
After they see the signal flare to return, they mistakenly believe the mission is successful and make plans to leave. During their departure, they think they see Levi returning to them, but it turns out to be an unexpected assailant. Gunther Schultz is killed by a disguised Annie Leonhart who then transforms. The remaining members instruct Eren to escape, and engage the Titan. Despite an impressive coordinated attack, the Female Titan turns the tables and proceeds to kill the remaining members of Levi's original team, Petra Rall, Oruo Bozad, and Eld Gin. Eren transforms to kill the Female Titan in revenge, but is defeated, and needs to be rescued by Levi.
Some time after the Wall Rose invasion, Captain Levi selects a number of Scout Regiment to fill out the new Squad Levi. Their first assignment as a squad involves hiding out in a remote cabin and safeguarding Eren Jaeger and Historia Reiss so that Eren could practice with his Titan without being noticed.
However, the squad receives word for a freeze on Scout activity and they evacuate the cabin before the arrival of the Military Police Regiment. Knowing that Eren and Historia are targets, the squad proceeds to Trost District in order to evade their pursuers. Jean Kirschtein is disguised as Eren and Armin Arlelt as Historia. The two decoys are kidnapped in their place, allowing the squad to track the kidnappers. The remaining members of the squad tail the kidnappers into a hideout, and incapacitate them when their leader arrives.
Elsewhere, three members from the Fourth Squad are attacked and killed by Kenny Ackermann and his soldiers while guarding the real Eren and Historia. Levi barely manages to escape and return to his squad, having to kill some of the MPs along the way. He then orders his squad to seize control of the carriage Eren and Historia are in. After Armin takes over the carriage, Jean is held at gunpoint by a Military Police soldier, who is then shot by Armin before she could kill Jean. They are forced to abandon the carriage soon afterward as they are nearly ambushed by more Military Police members who are using Anti-Personnel omni-directional mobility gear. As their opponents flee with Eren and Historia, Mikasa Ackermann tries to follow them but is restrained by Levi.
Unsure of Eren and Historia's location and now, also made fugitives of the law, squad Levi camps in the woods outside Stohess District. The squad plan to infiltrate the brigade, to gain directions to a Military Police checkpoint, in hopes of finding the captives. They capture Hitch Dreyse and Marlo Freudenberg, though they prove to be cooperative, and offer to show them the way to the checkpoint themselves.
Hitch and Marlo lead Squad Levi to the least manned checkpoint, which the squad then charges with the use of horses and a wagon. They break through and Levi captures a member of the Interior Police. Levi interrogates the man into the night although he denies having any knowledge about Eren and Historia's location. Sasha hears someone approaching and the squad quickly take cover. It turns out to be Hange, who brings the news that the charges on the Scouts had been lifted, then reveals they were also able to deduce Eren and Historia's location; a village chapel that Rod Reiss had rebuilt after an alleged burglary had taken place there.
Squad Levi arrives at the chapel and find a secret door leading to the underground. Levi and the others make preparations for facing the Anti-Personnel Control Squad, who are waiting for them below. The group sends barrels of gunpowder and bags of oil down the stairs, setting fire to them and filling the underground chamber with smoke, reducing visibility and the usefulness of firearms. Most of the squad exacerbates the problem with signal flares while Levi and Mikasa scout out their enemies. Levi calls for his squad to take them down and the team springs into action.
The squad dominate the following fight, and manage to force the enemy back to their last line of defense. Armin, alongside Moblit, are left with Hange after they are injured by Caven. Meanwhile, Levi and company head towards the net dropped by the interior police in their retreat, though their attention is grabbed by the light of a Titan transformation. The squad quickly venture deeper into the cavern as it collapses around them.
Eventually, they locate Historia and Eren, atop a pedestal. The squad frees Eren from his chains, but find no way to escape. After being told to make a choice by Levi, Eren decides to transform into a Titan, and seals up the collapsing cavern by using his newly acquired hardening power. Sasha Braus and Conny Springer locate an exit from the cavern and the squad meet up with the rest of the Scouts while in pursuit of Rod's humongous Titan.
The Abnormal Titan crawls towards Orvud District where the military prepare their strategy. Levi informs Historia of the plan to install her as Queen in the near future. Conny and Jean protest this, not wanting her forced into another role just after she has broken free of her father, but Historia agrees. When Historia attends the meeting she arrives geared for combat and takes her place among the rest of Squad Levi.
As the threat from the Titan becomes imminent, the Special Operations Squad set up a net of explosive barrels for use against the gigantic Titan. After the Titan comes within range, Armin and Sasha use ODM to reel carts filled with explosives into the Titan's hands and Eren shoves the net into its open mouth, where the heat of the Titan is enough to cause the explosives to spontaneously combust. The Titan explodes into numerous pieces and the squad flies out to cut the piece containing the nape. Historia lands the killing blow herself.
During the operation in Shiganshina District, Squad Levi splits up when Armin reports to Erwin about finding three cups, tipping him off regarding Reiner, Bertholdt, and a third person. Armin is placed in charge of a team to search around the inner gate for enemies. Meanwhile, the rest of the squad is ordered to wait on standby atop the Wall. After Reiner is located and injured by Levi, he transforms into the Armored Titan.
Commander Erwin orders Squad Levi and Squad Hange to take down the Armored Titan, however, Levi himself is instructed to help guard the horses. Armin rejoins Squad Levi as its interim leader. Erwin gives orders to use Eren as bait in order to lure Reiner away from the horses. This plan is carried out successfully, leading to the two Titans engaging each other.
At a stalemate during the fight, Squads Hange and Levi use the opportunity to surround Reiner and use the Thunder Spears to blind, shatter, and then defeat the Armored Titan. The squad grieves over Reiner, lamenting the lack of opportunity for any negotiations. When Bertholdt is thrown over the Wall, the two squads pull back from the area. However, he does not cause an explosion as expected, and Armin seizes the opportunity to negotiate with him. When the negotiation fails, Bertholdt uses his ODM gear to sling himself skyward and transforms. The energy creates a devastating blast that rips through Shiganshina.
The squad takes cover before regrouping. As they watch the Colossal Titan spread flaming wreckage across Shiganshina, Armin hesitantly gives an order to fight a war of attrition against the Colossal Titan. However, Jean points out the flaws in this plan. This makes Armin ask him to take over command. The squad then temporarily moves to the river.
Jean has Eren yell to draw Bertholdt's attention, however, he is ignored and Bertholdt continues toward the Wall. Eren, under Jean's order then attempts to push back the Colossal Titan, but fails, as Bertholdt kicks him to the top of the Wall, incapacitating him. The rest of the squad attempts to fight Bertholdt using a diversionary tactic, however he sees through this plan and repels both the squad and Mikasa's Thunder Spears using steam. Suddenly, to the squad's shock, the Armored Titan emerges, ready to rejoin the fight.
Armin notices the Colossal Titan is thinner, and forms a plan for him and Eren to take it down. He requests the rest of the squad draw Reiner away, before traveling up the Wall to wake Eren.
As Eren and Armin prepare for the rematch, the rest of the squad engages Reiner. Mikasa cripples his leg, immobilizing him in place. Jean comes up with a plan and uses himself as bait so Sasha and Conny can dive in to blow the hinges of Reiner's jaw. However, Reiner strikes a nearby rooftop and the debris hits Sasha and Jean, making Sasha's Thunder Spear miss its mark. However, Hange returns in time and hits Reiner's jaw in Sasha's place, giving Mikasa the opportunity to blow Reiner out of his Titan's nape. Armin and Eren successfully take down Bertholdt, though Armin is burnt beyond recognition.
Levi also returns from his side of the Wall, having chased the Beast Titan along the way. The rest of the squad rest as Reiner is interrogated by Hange. They debate whether to kill Reiner, or steal the power of the Titans from him. Hange is uncertain all the criteria have been met for using the Titan injection, but Jean convinces them that they still need answers in order to face their enemies and that it is worth trying to steal his power instead of killing him outright. Mikasa is sent off to scout the situation and locate Levi, while the others wait. If she cannot get the injection from Levi, she is to signal for Hange to kill Reiner.
After finding Eren, an unconscious Bertholdt, and the mortally wounded Armin, Mikasa fires the signal flare since Armin meets all the conditions for receiving an injection. However, before Hange can kill him, the Cart Titan charges at them. Jean tackles Hange out of the way and the Cart Titan runs off with Reiner in its mouth. The Special Operations Squad reunites amid a violent confrontation between Eren and Mikasa against Levi, over the Titan injection. Levi plans to inject Erwin and have him eat Bertholdt, and orders the squad to clear the area to accomplish this. However, Levi changes his mind, and injects Armin instead. Eren, Mikasa, Jean, and Conny help Armin out of his Titan. After this, the squad separates, searching the battlefield for survivors but finding none. A few Survey Corps members clear the basement before the nine survivors return to Trost.
Several months pass and eventually all the remaining Titans within Wall Maria are killed or destroyed and people return to repopulate Shiganshina District. The Special Operations Squad then sets out for the first expedition beyond Wall Maria in six years. While many of them are surprised by the lack of Titans in the area outside Wall Maria, Hange theorizes that it is due to the majority of the Titans invading Wall Maria five years prior. They eventually reach a Marleyan military structure where Eldians were taken to and turned into Titans. Beyond that, they finally reach the coast and bear witness to the sea for the first time, the only thing now separating them and the nation of Marley.