"Zegapain" is a science fiction anime series set in a world where humanity faces extinction due to an alien force known as the Gards-orm. The story centers on Kyo Sogoru, a high school student who initially believes he is living an ordinary life. However, his reality is shattered when he encounters Shizuno Misaki, a mysterious girl who reveals that the world he perceives is a virtual simulation created to preserve human consciousness. The real world has been devastated by the Gards-orm, and humanity survives only within this digital construct.

Kyo is recruited into a resistance group called Cerulean Guard, which fights the Gards-orm using advanced mechs called Zegas. These mechs are piloted by individuals who retain their memories of the real world, unlike most humans who are unaware of the simulation. As Kyo becomes more involved in the conflict, he discovers that his own memories are fragmented and that his past is deeply connected to the ongoing war. Shizuno, who serves as his guide and ally, harbors her own secrets about the nature of the simulation and the true purpose of the Cerulean Guard.

The narrative explores themes of identity, memory, and the nature of reality as Kyo grapples with the duality of his existence. He must reconcile his life in the simulated world with the harsh truths of the real one, all while battling the Gards-orm to ensure humanity's survival. Other key characters include Ryoko Kaminagi, a skilled Zega pilot with a strong sense of duty, and Lu Sheng, a scientist who plays a pivotal role in understanding the simulation and the enemy.

The plot unfolds through a series of battles, strategic maneuvers, and revelations about the origins of the Gards-orm and the simulation. As Kyo and his comrades fight to protect the remnants of humanity, they uncover deeper layers of the conflict, including the possibility of coexistence with the Gards-orm and the ethical implications of their actions. The series balances intense mecha action with philosophical undertones, creating a narrative that is both engaging and thought-provoking.