The Sidonia has engaged a new type of Guana. This armored-type is strangely aggressive, and most of the young pilots who have confronted the monster are not prepared for this change in stragedy.

Rookie pilot Nagate Tanikaze has even fewer completed flight-hours, but that does not prevent him from devising his own plan of attack when his squadron is in danger. Feeling the stirrings of a bond that is precarious at best given that humanity itself is in peril, he ignores orders to save a colleague left behind.

And then upon returning to the Sidonia, the history of the Guana is revealed to Tanikaze, not long before battle and a rival's jealousy leaves him alone in space again.