After leaving his underground shelter deep within the spaceship Sidonia, Nagate Tanikaze is spotted by security while attempting to steal some rice.

After Eiko is killed, Nagate regains consciousness and fends off the Gauna against orders and without the right weapons.

Nagate explores Sidonia and becomes friends with Kunato while trying to defend another friend. The Gauna attack and the experienced pilots are forced to take action.

While trying to outrun the Gauna, Captain Kobayashi orders an emergency evasive manoeuvre that causes massive casualties in Sidonia's residential district.

Nagate locates Shizuka, but the Tsugumori runs out of power and the pair are left adrift. After days in space, food and water are gone and they are in dire straits.

After Shizuka and Nagate return to Sidonia, they are celebrated as heroes. Nagate, Shizuka, Kunato, and Ren Honoka are made official Guardian pilots for their services in the battle against Gauna 487.