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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.

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.

Jax and the team visit the distant planet where Professor Osborn first discovered Jax as an infant during the Earth-Zatarian War in an attempt to find the Ancients in the hopes of saving our Universe. But is dealt a tragic blow when Ralen suffers a loss that will change him forever.

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.

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.

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.

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.

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.

Xander, Ralen, and Jett discover and track a consignment of illegal weapons to a freighter captained by a desperate cargo pilot, Roy Scantron, where they discover the cargo is clones of dead EarthCom soldiers.

Xander, Ralen, and Jett finally return to Earth, only to find it completely devoid of life with the exception being a mysterious and amnesic Jax; now they will need to work together to unravel the strange mysteries of this surreal world.

Jax and the team go in search of a lost alien race that may be the key to saving the universe, but they find themselves plagued by disturbing nightmares that arise out of each individual's personal traumas and most personal fears.

Jax races against time to save the Universe from complete destruction before the Ancients can render their final judgment, as Xander covertly pursues his own plans for redemption.