Jax and Xander, now both working for the Earth Confederacy Intelligence Services, attempt to track down the fugitive Tierney and discover she is searching for a destructive weapon that can potentially destroy the entire Universe. Meanwhile, Jax comes face-to-face with a woman she never expected to see again: her mother, Eve.
Jax, Xander, Ralen, and Matta track the fugitives Tierney and Jax's mother, Eve, to a remote planet with a mysterious secret, only to come into the crosshairs of the planet's strange religious cult, who will stop at nothing to maintain their sinister order.
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.
Jax and the team go in search of a lost alien race that may be the key to saving the Universe, but on the way, find themselves plagued by disturbing nightmares that arise out of each individual's personal traumas and most personal fears.
Xander and Jett set out to save Ralen, who has gotten caught up in the high stakes world of an intergalactic fight club. Meanwhile, Jax is on a mission for Osborn to acquire intel from a beautiful Sumi princess who is about to get married, but finds herself falling for Jax.
Xander, Ralen, and Jett help defend a mining colony in the Outer Rim that is under constant siege from Sumi Pirates. Meanwhile, back at the Academy, Jax is recruited by Osborn for a secret mission.
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.
As the Galaxy sits on the brink of war, Jax and the team must unite all the races of the Galaxy in the hopes of preventing their destruction. Meanwhile, Osborn grapples with the ghosts of his past.
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.