The high school setup is bait. By episode 12, the show has already rewritten what you think you're watching, and it keeps going deeper. Zegapain builds a philosophical trap that catches you in the same existential horror as its characters, then forces you to sit with what that means for everyone involved. The romance isn't a subplot, it's the only thing that matters when you realize nothing else is real.
Kyo just wants to save his school's swimming club. As the only member, he's running out of time before the student council shuts it down for good. When he convinces the mysterious Misaki to help with a recruitment video, she agrees on one condition: he has to pilot a mecha for Celebrum, an underground military organization fighting invaders called the Gards-orm. These aliens have already carved out dangerous zones across the planet, and humanity's only real defense seems to be Kyo himself. The catch is that nothing about this feels new to Kyo. Piloting the mecha triggers fragmented memories that shouldn't exist, moments that feel lived but impossible. As he keeps fighting alongside Misaki and his friend Ryoko, Kyo realizes something fundamental is wrong with reality itself. The line between his ordinary high school life and this war against alien occupation starts to blur in ways that force him to question everything: his past, his present, and whether any of it is real.