Shin and his friends continue their pursuit of Morpho, but are continually hampered by Legion reinforcements. Anju, Theoto, and Kurena elect to stay behind to delay the Legion or provide long range support, while Raiden is wounded protecting Frederica. Shin orders Frederica to stay with Fido while he confronts Kiriya alone. Shin manages to hold his own against Kiriya, but his cannon is damaged, leaving him with only a single shot, and Morpho’s capabilities make it so Shin has trouble getting into close range with Kiriya. However, Shin is assisted by long range missile fire from an unknown source, damaging the Morpho and distracting Kiriya. Kiriya is further distracted when Frederica arrives on the battlefield, begging him to stop. Kiriya however is still too consumed with rage, so Frederica points a gun at herself. Shocked, Kiriya moves to stop Frederica, giving Shin the opening he needs to get into point blank range of the Morpho and destroy Kiriya’s core. Frederica then has a vision of Kiriya entrusting her care to Shin before being escorted to the afterlife by Shourei. Back in reality, Kiriya’s death causes Morpho’s self destruct to activate and it explodes with both Shin and Frederica still in the blast radius.

Shin and his friends continue their pursuit of Morpho with Frederica in tow. Meanwhile, the Federacy and its allies begin staging diversionary attacks on the Legion to draw their attention away from Shin. Grethe returns to the frontlines with the rest of Nordlicht, now freshly resupplied and ready to support Shin. In Legion territory, Raiden confronts Shin over his recent behavior during battles, warning him that such a dangerous fighting style puts them all at risk. He reminds Shin that they are still a unit, and his friends will be there to support him so he doesn’t need to keep fighting alone. As the team continues to chase Morpho, Frederica asks everybody about the ocean and they all promise to go see the ocean together after the war. That night, Frederica meets with Shin and confides that like him, she fears losing her sense of purpose, and she deluded herself into thinking that she needed to put Kiriya to rest. She tells Shin that he shouldn’t be afraid of the uncertainty of the future as long as he has his friends. However, Shin reveals that ever since his near death experience at the hands of Shourei, he has been unable to feel any desires, and thus doesn’t feel he is even alive. Elsewhere, No-Face warns Kiriya that enemy forces are tracking him and instructs him to deal with the matter.

As the Nachzehrer nears the Morpho, it comes under anti-air attack, forcing Nordlicht to airdrop while the Nachzehrer pulls away to distract the Legion’s air defenses. Nordlicht then fights its way through the Legion defenders and approaches the Morpho, only for Shin to realize at the last second that the damaged Morpho is bait to lure them into the range of a second Morpho gun controlled directly by Kiriya. Nordlicht is narrowly able to avoid the Morpho’s shot and retaliate. Shin falls back into his battle lust, and is only knocked out of it when Kurena is forced to fire on him. With the element of surprise lost, Kiriya is ordered by his superior “No-Face” to withdraw. Shin and his friends decide to pursue Kiriya while the rest of Nordlicht stays behind to hold back the Legion reinforcements. Meanwhile, as the main Federacy force advances, they manage to recover Grethe and the Nordlicht survivors, but cannot provide any support to Shin. As Shin and his friends take a break, they discover that Frederica has stowed away in Fido’s cargo trailer. While they are angry at her coming along with them, they have no choice but to bring her along with their pursuit of Kiriya.

As Nordlicht prepares for their mission, Grethe successfully petitions to allow the use of the prototype ground effect airplane “Nachzehrer” to be used as the unit’s transport, rather than relying on much slower and more vulnerable helicopters. Grethe also volunteers to be the Nachzehrer’s pilot, being the last remaining person with any experience flying it. Frederica unsuccessfully tries to convince Shin not to go on the mission, fearing that he will die or become a monster like Kiriya. Zimerman, powerless to stop the operation, expresses his wish to see that Shin and his friends return home alive no matter the cost, and privately swears to himself he will destroy the world if they don’t. The Federacy and its allies then commence an all out assault on the Legion as a distraction, opening a hole in the Legion’s defensive perimeter allowing the Nachzehrer to launch and head for the Morpho. During the flight, Shin hears the Black Sheep’s voices and smiles.

In the Republic, Lena organizes a desperate last stand against the invading Legion. In the Federacy, Shin, his friends, and Frederica manage to survive the bombardment, but it is revealed that the Legion used a massive railgun codenamed “Morpho” to bombard all of the Federacy’s forward bases, inflicting significant losses. While Morpho was damaged by a cruise missile attack, military analysts predict it will be able to move into range of any allied capital city once it is repaired. With few options due to Morpho’s extreme range, the Federacy decides to send Nordlicht on a deep strike mission to destroy the railgun. While Grethe is furious the military is sending Shin and his friends on what is expected to be a suicide mission, none of them object since they’d rather go down fighting the Legion rather than run away from the war like the Republic did. Meanwhile, Shin’s friends are worried about his mental state after he received a letter from Eugene’s sister angrily demanding to know why he killed her brother and the possibility of Lena being dead. A week after the Legion invaded, the Republic’s capital and Lena’s home are shown to be in ruins.

The Legion begins a simultaneous offensive against the Federacy, Republic, and other allied nations with massive numbers never seen before. The Federacy’s defense lines come close to being overun, but a quick deployment and counterattack by Nordlicht squadron manages to slow them down long enough for Federacy lines to reinforce and stabilize. Shin the goes on the offensive against the Legion, destroying countless Legion units on his own. Frederica has a vision and witnesses Shin taking pleasure in the fighting, reminding her of Kiri’s fall to madness. She also witnesses the Republic’s defenses collapsing under a major Legion assault. Eventually, the Legion withdraws from the Federacy and Frederica warns Shin about his similarity to Kiri. Meanwhile, in the Republic, word of the Legion breakthrough reaches HQ, so Lena’s uncle agrees to try and hold off the Legion long enough for Lena to rally the 86s to close the breach. Using an upgraded Para-RAID, Lena connects herself to every 86 pilot simultaneously. Back in the Federacy, Frederica informs Shin and his friends about the dire state the Republic is in when both Shin and Frederica sense Kiri is about to bombard their base.

With Federacy analysts predicting a massive Legion offensive, the Federacy military decides to reorginize its forces in order to prepare for the attack. Grethe takes the opportunity to reunite Shin and Nordlicht Squadron, who had been previously split up to assist other units. Grethe briefs Nordlicht about the coming Legion attack, as well as the discovery of several surviving countries, but they still haven’t gotten any response from the Republic. Shin submits his comments about the Reginleif’s performance as well his own warning of the Legion attack, though Grethe is skeptical about the number of Legion he is describing. Frederica visits Shin and tells him more about Kiriya, who was part of the Nouzen clan and is Shin’s distant relative. She reveals that after the Empire declared war on its neighbors, the people rebelled against the royal family. Since the Legions were not designed to combat domestic rebellion, the royal family was forced to rely on their personal guard, and Kiriya eventually went insane trying to fight off the rebel army. Eventually, Ernst was able to capture Frederica and faked her death. Believing Frederica was dead, Kiriya allowed himself to be taken by the Legion. Frederica then cautions Shin that he should seriously think about his future, which reminds him of Lena. Meanwhile, in the Republic, Lena continues preparing for the Legion attack, who are closing in to the Republic’s borders.

Thanks to their experience, Shin and his friends manage to pass officer training and are assigned to the Nordlicht Squadron under the command of Lt. Colonel Grethe Wenzel. Grethe takes Shin and his friends to a location recently reclaimed by the Federacy, where they have recovered their wrecked Juggernauts and erected a memorial dedicated to all of the names Shin had gathered. Grethe also reveals that when they recovered Fido’s wreckage, they found its core still intact so they built it a new body. Frederica joins the unit as well as their official mascot, and she returns Shin’s handgun to him. Shin and Nordlicht soon begin assisting the Federacy forces by piloting the Reginleif mechs, based on the Juggernaut design. During the fighting, Shin reunites with Eugene, another Federacy officer who he befriended before signing up who joined the army to make a better life for his sister. However, after a Legion attack, Shin comes across a mortally wounded Eugene and is forced to mercy kill him. Afterwards, Shin receives word that the battle is going poorly and to prepare for yet another Legion attack.