In the year 2029, Niihama City has become a technologically advanced metropolis. Due to great improvements in cybernetics, its citizens are able to replace their limbs with robotic parts. The world is now more interconnected than ever before, and the city's Public Security Section 9 is responsible for combating corruption, terrorism, and other dangerous threats following this shift toward globalization. The strong-willed Major Motoko Kusanagi of Section 9 spearheads a case involving a mysterious hacker known only as the Puppet Master, who leaves a trail of victims stripped of their memories. Like many in this futuristic world, the Puppet Master's body is almost entirely robotic, giving them incredible power. As Motoko and her subordinates follow the enigmatic criminal's trail, other parties—including Section 6—start to get involved, forcing her to confront the extremely complicated nature of the case. Pondering about various philosophical questions, such as her own life's meaning, Motoko soon realizes that the one who will provide these answers is none other than the Puppet Master themself.

At the behest of Admiral Yang Wen-li, defected intelligence officer Commander Baghdash makes an emergency broadcast announcing that the National Salvation Military Council staged a coup under the direction of the Galactic Empire. Despite the lack of physical evidence, this debilitating declaration inspires former Rear Admiral Andrew Lynch to reveal his own role in sowing discord within the Free Planets Alliance. A fatal shootout between Lynch and Admiral Dwight Greenhill acts as the final death knell to the short-lived period of martial rule. Within the Galactic Empire, footage of Duke Otto von Braunschweig's nuclear bombing of Westerland results in the dissolution of the Lippstadt League. Marquis Reinhard von Lohengramm's decision to allow the massacre for personal gain creates a rift between him and High Admiral Siegfried Kircheis, souring the taste of their inevitable victory. Now on the cusp of achieving absolute power, Reinhard is embattled by his apparent personal failings and the heavy responsibilities of leadership. Though the civil wars in both the Alliance and the Empire are coming to a close, neither side can ever regain what is lost. Yang Wen-li and Reinhard von Lohengramm each take bitter solace in the knowledge that just on the other side of the galaxy is a worthy opponent—and a true equal.

The Free Planets Alliance's invasion of the Galactic Empire has failed after supply mismanagement led to heavy losses. Unwilling to abort the expedition despite being greatly outnumbered, Fleet Admiral Lazar Lobos orders the remaining Alliance fleets to gather in the Amritsar Starzone for a final stand against the incoming counterattack. Strategic genius Fleet Admiral Reinhard von Lohengramm leads the Imperial forces into this decisive battle with an overwhelming advantage. However, his rival, tactical magician Vice Admiral Yang Wen-li of the Alliance, once again makes up for the incompetence of his superiors and stages a narrow escape for himself and his fellow soldiers. Though both Reinhard and Yang are displeased with the outcome—the former for his imperfect victory and the latter for the tremendous casualties—their attention must turn to the bubbling political unrest on both sides of the galaxy.

As Yang is ordered to appear before the Free Planet Alliance, he’s shaken by the corruption he discovers. Meanwhile, Marshal Reinhardt uncovers disloyalty under his command as an upstart admiral launches a vicious offensive to retake the Iserlohn Fortress. Struggling to make strides in this never-ending bloody war, these two finally see their true enemy lies not from without—but from within! (Source: Crunchyroll)