After the death of her parents, Jax matriculates at the Fleet Training Academy on Earth where she learns to defend the Galaxy from intergalactic threats and makes a new family of friends, but also makes a shocking discovery about her own identity.

When Atria Nine learns that Adari leader, Seeker Creston Hubbell, will be speaking on campus, she enlists the help of Jax and the study group to stand up against her former masters to help free her clone sisters and brothers from oppression on her homeworld.

A war veteran from the legendary space battle cruiser Sea Hawk makes a shocking revelation to Jax and Greg that could lead Jax to discover who actually killed her parents.

Jax joins Xander and her fellow cadets in responding to an emergency distress call from a secret lab, only to discover that a deadly experiment has infected the scientists and the cadets.

Thomas's telepathic father arrives on campus and tries to enlist his estranged son in a dangerous heist in which nothing is as simple as it appears.

When Pilar's bio-organic implants are hacked, Jax and Ralen lead an investigation to help save their friend and find out who's responsible and stop them from continuing to torment Pilar.

When Xander enlists Jax on a dangerous mission in which she must rekindle a relationship with an old flame, Xander, must confront his own feelings for Jax and question if all orders are meant to be obeyed.

Trapped on an alien world, Jax, Xander and Ralen are stranded with no way home. They must band together to survive, but divided loyalties threaten to destroy them from within. And Jax will ultimately be forced decide her allegiances if they make it through the long night.

Ralen is on trial for his life after being accused of having sabotaged the Tereshkova. But even Jax has her doubts about Ralen's veracity when his wife arrives from Zatar to defend him.

As the Fleet Academy, students prepare to celebrate Armistice Day (the anniversary of the end of the Zatarians war), Jax continues to struggle with the revelation that Ralen is married. Meanwhile, Ralen must decide where his loyalties truly lie.

Jax and Xander have their hands full as a dangerous cat-and-mouse game erupts on campus. Various parties from across the galaxy arrive on Earth, all in pursuit of Jax, during which she encounters a surprise ally who not only protects Jax, but also sheds light on who she really is. Meanwhile, Atria joined by Pilar, bravely explores her new life mission on Adar, helping her clone brothers and sisters, while Thomas searches for his missing father and Ralen contemplates his return to Zatar.

Picking up the pieces from the attack on the Fleet Training Academy by Leone Vokk, Jax and Xander must confront Tierney to stop her sinister plans for galactic domination while Atria's grassroots movement on Adar to run for Seeker may have serious consequences for the clones as well as her friends.