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.
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.
Pilot Nagate Tanikaze is now renowned for his actions in the recent battle, but Nagate is more concerned with the disappearance of the ena Hoshijiro.
Nagate and his team fight a hard battle against Gauna 549, aided by the appearance of a new type of gauna calling itself Tsumugi Shiraui.
Having disposed of the opposition, Kobayashi sets Sidonia's course to the ninth planet in the nearby Lem System. All-out war now seems unavoidable.
A new threat appears in the form of Gauna 550, which has ejected countless lesser gauna cores on an intercept trajectory with Sidonia.
Despite being instrumental in their victory, Tsumugi is severely damaged defending Sidonia. Izana, also critically injured, makes a bold decision.
Evicted from his dorm and with nowhere to go, Nagate asks to stay with Izana for a night; Tsumugi has an emotional crisis triggered by a close call.
The Sidonia's new weapon test succeeds, but the crew realizes they can't shut it down; Yuhata sends the garde pilots to investigate the disturbance.
The pilots and Tsumugi repair damage to the Sidonia following the Gravitational Beam Emitter incident; Tsumugi is upset for causing a minor accident.
Izana finds out her "date" with Nagate was a setup and storms home. Soon after, she is called to be part of a team that will scout out Planet Nine.
The reconnaissance team is attacked by the gauna; Izana and the squad leader manage to escape into the atmosphere of Planet Nine.
Izana and the recon squad leader are pursued by an enormous humanoid gauna. Meanwhile, Tsumugi faces off against the Crimson Hawk Moth.
Nagate rescues Tsumugi but is overpowered by the Crimson Hawk Moth. The situation looks grim as swarms of gauna bear down on the survivors.