In isolation his entire life, Nagate must adjust to life in a centuries-old space colony while training as a cadet pilot to fight an ancient threat.

Nagate is haunted by his first combat experience against the Gauna. Later, he meets the elite pilots of Sidonia.

Exploring Sidonia, Nagate makes an enemy of Kunato while protecting a friend. The Gauna attack, calling the pilots into action.

After a disaster aboard Sidonia, Nagate and his team are ordered to retrieve a valued weapon. He later defies orders to save a friend.

Nagate and Shizuka, adrift in space, slowly run out of supplies as they await rescue from a departing Sidonia, which is too far away to send help.

Nagate and his squad graduate as pilots and are quickly sent into combat when the enemy returns; Kunato explores Nagate's history.