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.

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.

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.