In Cour 1, it is revealed that the Legion surpassed its programmed shelf-life by harvesting the brains of fallen soldiers to assimilate their neural structures into specialized "Black Sheep" and "Shepherd" units. Shin can hear their distress frequencies because a childhood near-death experience altered his neural synchronization. When Spearhead is ordered on an open-ended reconnaissance mission into deep Legion territory—a purge engineered by the Republic—Shin confronts and destroys the Shepherd unit holding the mind of his brother Shourei, setting him free.
In Cour 2, the five survivors (Shin, Raiden, Kurena, Anju, and Theo) are rescued by the Federal Republic of Giad and adopted by Provisional President Ernst Zimmermann. Unable to adapt to peacetime, they voluntarily reenlist and pilot Reginleif units alongside child Empress Frederica Rosenfort. They face the Legion's catastrophic railgun unit, the "Morpho," piloted by Frederica’s former guardian, Kiriya Nouzen. Simultaneously, the Legion breaches the Republic's Gran Mur; San Magnolia collapses, leaving Lena to lead surviving 86 soldiers in guerrilla defense.
During the final offensive against the Morpho, Shin falls into suicidal frenzy but defeats Kiriya. Trapped in his wrecked cockpit and awaiting death, Shin is visited by an arriving Republican officer—Lena, who does not recognize him due to his obscured speaker and having never seen him. Lena tearfully confesses that the Spearhead Squadron taught her to live with dignity and vows to keep surviving to catch up to the "Undertaker." Her words restore Shin's will to live. In Episode 23, Lena arrives in Giad to command an independent strike force, where she and the five Spearhead survivors are joyfully reunited face-to-face.