After the death of her parents, Jax matriculates at the Fleet Training Academy on Earth, where she learns to defend the galaxy; Jax makes a new family of friends and a shocking discovery about her own identity.
When Atria Nine learns that an Adari leader will be speaking on campus, she enlists Jax's help 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.
Still struggling from the loss of a close friend, 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.
Thomas' 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 stop those responsible from continuing to torment Pilar.
Jax discovers a deadly secret from her past that she is desperate to understand with the help of Ralen and Pilar; the CIS grows increasingly suspicious of Xander's divided loyalties.
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 questions if all orders are meant to be obeyed.
Jax, Xander and Ralen must band together to survive while stranded on an alien world, but divided loyalties threaten to destroy them from within.
Ralen is on trial for his life after being accused of having sabotaged the Tereshkova; 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, Jax continues to struggle with the revelation that Ralen is married; 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; Jax encounters a surprising ally who not only protects her, but also sheds light on who she really is; Thomas searches for his missing father.
Jax and Xander must confront Tierney to stop her sinister plans for galactic domination; Atria's grassroots movement on Adar to run for Seeker may have serious consequences for the clones as well as her friends.