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.

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

The enemy is revealed to be even larger and deadlier than previously believed, resulting in three squads engaging in a deadly fight.

Nagate is blamed for a defeat and harbors guilt over a casualty; the early years of Sidonia are revealed.

The Gauna find a distressing way to demoralize and out-fight the attack force. Nagate returns to Sidonia with a prize that may help in the fight.

Nagate fights one-on-one with the heart of his enemy while the strike force does not fare well in its attack on the Gauna.