Após a morte de seus pais, Jax se matriculou na Academia de Treinamento da Frota na Terra, onde aprende a defender a galáxia de ameaças intergalácticas e faz uma nova família de amigos, mas também faz uma descoberta chocante sobre sua própria identidade.

Quando Atria Nine descobre que a líder do Adari, Seeker Creston Hubbell, estará falando no campus, ela pede a ajuda de Jax e do grupo de estudo para enfrentar seus antigos mestres para ajudar a libertar suas irmãs clones e irmãos da opressão em seu mundo natal.

Um veterano de guerra do lendário cruzador espacial Sea Hawk faz uma revelação chocante para Jax e Greg que poderia levar Jax a descobrir quem realmente matou seus pais.

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.

Jax discovers a deadly secret from her past that she is desperate to understand with the help of Ralen and Pilar while the CIS grows increasingly suspicious of Xander’s divided loyalties.

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.

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.