1Les Choses ont Changé
Jax et Xander, qui travaillent désormais tous deux pour les services de renseignement de la Confédération terrestre, traquent la fugitive Tierney et découvrent qu'elle recherche une arme destructrice qui peut potentiellement détruire l'univers entier.
2Ne Réfléchissez pas à Deux Fois, Tout Va Bien
Jax, Xander, Ralen et Matta suivent la mère de Jax, Eve et Tierney, jusqu'à une planète lointaine, dans l'espace inexploré du système Horatius. À leur arrivée sur le Monde de Clayton, ils découvrent l'un des vaisseaux de l'Arche, le Clayton, qui faisait partie de la Grande Migration venue de la Terre 150 ans plus tôt. Sur la planète, ils découvrent les origines des premiers voyageurs, mais se retrouvent dans le collimateur de leur étrange secte religieuse. Le petit groupe découvre bientôt que la secte est prête à tout pour maintenir son ordre sinistre. Pendant ce temps, de retour à l'Académie de Formation de la Flotte Earthcom sur Terre, après avoir reçu une seconde chance, Jett commence à semer la zizanie, mais finit par mettre à rude épreuve ses relations, notamment avec Zazie. Des secrets sont révélés par Eve et Jett.
3Gates of Eden
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.
4Beyond Here Lies Nothin'
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.
5On a Night Like This
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.
6Pay in Blood
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.
7A Fool Such As I
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.
8Tell Me that It Isn't True
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.
9All Along the Watchtower
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.
10I Forgot More Than You'll Ever Know
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.