A mysterious girl named Eureka arrives at the home of Renton Thurston looking for the Amita Drive, necessary for the proper functioning of her LFO the Nirvash, throwing his life into chaos.
The Council of Sages discusses the Nirvash's immense display of power and how it is connected to Adrock Thurston--Renten's father. Meanwhile, Renton joins Gekkostate to get closer to Eureka, only to find himself at the bottom of the organization.
When a shopping trip with fellow Gekkostate members Talho and Hilda turns ugly, it's up to Renton to pilot an LFO solo for the first time in order to keep everyone form getting into too much trouble.
Eureka's "kids" pull a series of pranks on Renton, dead-set on keeping anyone from getting too close to the woman they call "Mama." Meanwhile, Renton goes out on a dangerous mission without authorization from the rest of Gekkostate.
Renton, Eureka, and the kids meet a member of the Vodarac religion while out shopping. Meanwhile the other members of the Gekkostate hunt a suspected terrorist. Things heat up when the two groups cross paths.
Gekkostate investigates a strange sphere that appeared in the sky. Eureka helps out, despite her declining health, and encounters a new Nirvash shows up--typeTheEND.
Eureka has merged with a scub, sending many of the crew into a panic. At the same time, Holland responds to a distress call and goes on a dangerous mission to rescue a Vodarac high priest.
The Vodarac priest that Holland rescued manages to remove the scub from Eureka's body, but the ordeal won't be without scars. Meanwhile, Renton tries to come to terms with the death and destruction he's caused since joining Gekkostate.
The Gekko crew tries to figure out the best way to tell Eureka that Renton has gone. Renton comes across Charles and Ray Beams and their carrier ship, the Swan, and decides to join them.
On his first mission with the Beams, Renton is faced with a difficult decision concerning the fate of a Vodarac girl. On the Gekko, Holland tries to avoid talking to Eureka about Renton, but he won't be able to avoid the subject forever.
Holland's quest to find Renton hits a snag when the Gekko runs into a military fleet preparing to take on the ship. Unable to wait, Eureka leaves to search for him on her own--but Renton might be closer than she thinks.
Holland prepares the Gekko for Ray and Charles' breaking in; locking Renton, Eureka and the kids in the safety of the brig under the excuse of disobedience.
A death in the battle between the Swan and the Gekko has major psychological consequences for members of both crews. Meanwhile, Holland reveals to Renton that he has a past connection to the Beams.
Renton's grandfather is put in charge of upgrades for the Nirvash. Improvements can't come soon enough, as an attack on the Coralians results in an all-out battle and the deployment of typeTheEND.
Gekkostate attacks the capital in order to rescue Norb, but Eureka's unwillingness to take any more lives hinders the operation. Colonel Dewey is quick to dismiss the assault, not knowing that Holland has succeeded in finding Eureka a partner.
Newly rescued Norb insists on returning to the Vodarac homeland, Eureka worries about improving her physical appearance, and Holland tells Renton about his first love--someone Renton knows all too well.
A misunderstanding between Renton and Eureka leads to awkwardness for the rest of the Gekko's crew. Meanwhile, Dewey continues his crusade against the Sage Council, and Stoner tries to improve public perception of Gekkostate through Ray=Out.
Eureka, Renton, and the kids finally make it to Earth, but have no idea what to do once they're there. Meanwhile Dewey takes Anemone to a celebration and tells her about his childhood and past with Holland.
Dewey is able to create a hole in the Scub Coral that Anemone can slip through. Will Dominic be able to stop her from carrying out her suicide mission?
The fate of the world is at stake as Eureka begins to turn into the next Scub Control Cluster. As an army of Coralians surround her, Renton understands that to save Eureka and everybody else, he might have to forsake his humanity.
