Renton Thurston is a 14-year-old boy, who leads a normal, yet boring and uninteresting life with his grandfather mechanic at a backwash town. One day, a mysterious mecha LFO referred to as the Nirvash typeZERO comes by their garage, and the pilot within is the most beautiful girl Renton has ever seen. But the next day, her arrival has attracted much of the United Federation Forces, and she is forced to stop them at any cost. Renton however makes the most life-changing decision in his life. Will he make it, and will he get the Amita Drive to the pilot of the Nirvash?

As the girl leaves to deal with the United Federation Forces, Holland, the leader of the Gekkostate, decides to get involved as well. Renton As the girl leaves to deal with the United Federation Forces, Holland, the leader of the Gekkostate, decides to get involved as well. Renton notices that the girl is in trouble, and his grandfather orders him to deliver the attachment known as the Amita Drive. He decides to use his REF-board to get to her, but will his foolish choice lead to something that he has never imagined before?notices that the girl is in trouble, and his grandfather orders him to deliver the attachment known as the Amita Drive. He decides to use his REF-board to get to her, but will his foolish choice lead to something that he has never imagined before?

With the pressure from the United Federation Forces, the Bellforest Airport is forced to immediately shut down. To make the situation worse, it leaves the Gekko, the Gekkostate's ship, completely trapped within the airport. As they find a way to get out of there, Holland, the Gekkostate's leader, decides to come and help them out. Meanwhile, Renton is faced with a life-changing decision as he is asked by Eureka to join her to become part of the Gekkostate.

Renton comes face-to-face with reality as his dream of being part of the Gekkostate finally comes true. However, the Gekkostate is having a serious issue with a shortage of monetary funds, which results in the whole group being broke. This leads to Renton becoming a part of a smuggling job and on his way to a drop-off point in the Nirvash with Eureka. But getting there won't be easy when they have to pass over a large military training base to reach their destination.

Renton tries his best to fit in with the group aboard the Gekko, but nothing he does seems to be going his way. Talho, meanwhile, takes him shopping in town and manages to find out a little bit about the things that trouble her.

Three kids aboard the Gekko, who call Eureka their mother, decide that Renton is their enemy and play several evil tricks on him. And when one of those tricks puts the whole ship in danger, Renton takes all three of them aboard the Nirvash to help, but they're all suddenly surrounded by a United Federation Forces KLF unit.

An entire squad of United Federation Forces KLF units are attacked by a mysterious enemy, so a report of the attack is sent to the Sage Council who summon someone from their past. Meanwhile, Renton leaves the Gekko as part of an important mission where he is supposed to secretly meet with someone and deliver a very dangerous package. What he doesn't know, though, is that he's being watched the whole time.

Eureka, Renton, and the kids meet an old woman named Tiptory while on a shopping trip. When they join her for a cup of tea, they're interrupted by Holland, who forces his way into Tiptory's apartment. Tiptory happens to be the key to an anti-government organization, which leads to the Gekkostate capturing her.

The Gekko arrives at Ciudades Del Cielo at the holy land of the Vodarac. The city itself is in ruins, but it's still called the "Beautiful City of the Sky." While they're there, Renton decides to have some fun lifting, but is interrupted when Holland punches him. This makes Renton fly away into the city crying. Afterwards, though, the beginning of a military bombing is signaled by sirens.

A massive amount of Trapar has erupted due to a tectonic shift that occured on the other side of the world. So, the Gekkostate group decide to go there to enjoy some lifting, but then end up at Monarchy, a Federation military base. Holland and Talho remember that life-changing place, which they'll never be able to forget - a past that Holland still can't put behind him.

Eureka's health continues to decline after realizing the connection between her and the Nirvash. At the same time, the Gekko encounters a strange phenomenon called a "Corallian." Despite her health, Eureka goes out in the Nirvash and is attacked by a new enemy - the Nirvash type "The End" - while inside the zone within the Corallian.

The type "The End" has attacked the Nirvash, and Renton has become unconscious and meets Eureka and Anemone in his nightmare. Meanwhile, outside the Corallian, the warship Izumo is involved in an intense battle with the Gekko.

Renton comes face-to-face with Anemone, the girl he met in his dreams, after returning from the Corallian Zone. Both Anemone and Eureka appear to be having intense headaches, making it seem as if the same thing is affecting them. So, Dominic and Renton go into the city to find medicine for them.

The Gekko has sustained heavy damage after a battle with the military. So they're forced to fly at a low altitude. The mystery surrounding Eureka continues to get stranger than ever as she gradually recovers after returning from the Corallian Zone, and Stoner provides his own explanation for it. Meanwhile, Dominic thinks about all the unanswered questions about Eureka and the Nirvash.

Renton goes to visit a town called Controrado, where he spent of his childhood, and takes Eureka to the house where he used to live. As he visits with people who knew his family, he hides the fact that he's part of the Gekkostate. The happy visit is soon interrupted when the United Federation Forces arrive.

The Gekkostate group hide inside a mine in order to repair the Gekko. Renton's frustration about Eureka's health forces him to say things he never meant to say. And as he enters a strange building in one of the tunnels of the mine, he once again experiences the nightmares from the Corallian.

Renton doesn't know what to do to make things normal again between him and Eureka, and the Gekko still is in need of repair. The Gekkostate does this by ordering some reflection film from a film craftsman. But once they get there, they find themselves forced to help catch the skyfish needed to make the film.

The group meets an old man named Breetani, who happens to be a digger, while they're in a mine. He reveals to them that he's been working in the mine for a long time. And Renton shows him the Nirvash, Breetani has an unexpected reaction.

As Eureka's mysterious illness persists, a United Federation Fleet is approaching the Gekko. The cause of her illness is suspected to be due to being close to the mines. For some unknown reason, though, Eureka decides to take the Amita Drive from the Nirvash, causing it to go into the depths of the mines with Eureka inside. This leads to Renton going after her, without ever realizing the tragedy that awaits.

Renton is worried about Eureka, who has now been partially absorbed by a scub. During this time, the Gekkostate get a distress call to rescue a Vodarac priest who's being held captive by the military. Holland accepts the job, but Renton accuses him of thinking that money is more important than Eureka is.

Eureka is being treated by the rescued Vodarac priest, and Holland uses what he says to drive Renton and Eureka further apart. Meanwhile, Renton's guilt is too much when he realizes all the people he's killed while fighting in the Nirvash, being apart from Eureka, and being mistreated by the Gekko crew. Instead of talking to them and discuss about their behavior, he decides to leave the Gekko, realizing the mistake he has chosen.

The crew has now been informed that Renton has left the ship, but nobody wants to be the one to tell Eureka. Meanwhile, Renton meets a couple named Charles and Ray Beams and invite him to live on their ship. They're revealed to be freelancers who do odd jobs for money. Renton sees Charles as a mentor and a friend who has the same interests. This makes it the first time Renton is actually happy in a long time.

Renton Thurston enjoys his life with Charles and Ray Beams, and they have been given a job; to travel to a city to pick up a Vodarac girl and transport her to the Vodarac Sanctuary, where she can rest in peace. Renton's intentions are different to that of the girl's parents, so he decides to go off on his own with the girl to find another city hospital. But humankind and its monstrous nature of hatred and prejudice, have become obstacles in Renton's way.

Due to having to make a bad landing on the Gekko, Holland has to have some minor injuries treated. As he and the doctor talk about Eureka, they realize how she still misses Renton and has taken over his job of running the store since he's been gone. Meanwhile, Renton finally learns about Charles and Ray's real mission, to which Renton can't believe.

As Renton walks to find a way back to Eureka after leaving Charles and Ray, he collapses at a nearby cottage, owned by a man named William. There, Renton was treated with hospitality, and soon finds out that he has a wife, Martha, who is diagnosed with "desperation disease." During his time with Will, he learns how the nature of the world around him is much more beautiful to settle in.