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

Pacifists endanger themselves by leaving the relative safety of Sidonia, while the enemy shows up larger and fiercer than before.

A large strike force encounters an enemy unit that takes them by surprise; Nagate does what he can to protect his friends.