Having narrowly avoided the collision with the asteroid, the Sidonia sets a course for the Lem system in order to wipe out the Gauna nest.

The Deep Sleep Capsules, technology that has allowed man to reach out to the stars. These chambers slow the aging process by 95%. A 20-year trip passes, and the traveler has only aged 1 year. It definitely has its advantages, but after you've been on a few trips, it sure gets very lonely. Right now, however, that's not the big issue. The year is 2264. The Syncam Corporation has sent the Saldes and its crew of 13 (and 1 cat) out into deep space to explore the potential of a newfound planet 20 years away. Soon after they awaken from their stasis, however, things are happening one after another. First, the crew learns that two of the crew are not who they claim to be. Then, one by one, crewmembers die suddenly. Then, the ship begins to turn against them. And as if it couldn't get any worse, they find another mess on their hands and it is ugly. What was supposed to be a simple exploratory mission has become a struggle for survival in the depths of space. 20 years from home, they're all alone and no one can hear them scream.

Three years since the end of their intergalactic excursion, both Lafiel Abriel and Jinto Linn have reunited; Lafiel as the captain of the attack ship Basroil and Jinto as her supply officer. The restart of the war between the Abh Empire and the Triple Alliance thrusts the inexperienced duo into the forefront of the deadly conflict. As the catastrophic battle between pure humankind and their greatest creation, the Abh, rages on, both sides accept that their conflict is not merely about territory, but about settling the inherent differences between themselves.

Due to a lack of ambassadors for the recently-conquered worlds the rapidly advancing fleet of the Bebaus brothers leave behind, Lafiel is appointed Territorial Ambassador of the planet Lobnas II. Upon arriving to the planet Jinto and Lafiel discover that the planet was used by the United Mankind as a prison planet and now has a million prisoners on the only inhabited island. The prisoners are parted in three blocks. The western where women are housed, the eastern belongs to the men and the central is mixed under the restriction that all prisoners living there are sterilized. The women in the western sector want to emigrate from the planet of fear for the men and when they do the men in the east rebel, overthrowing the guards and capturing Jinto to try to stop the emigration of the women. At the same time an enemy fleet heads toward the system forcing Lafiel to abandon Jinto.