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.

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.

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.

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.

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.