The year is AD 2225. Kouji Aiba and Aoi Housen are serving as astronauts in-training in Liebe Delta which is located on the edge of the Geduld Sea. When saboteurs with unknown intents suddenly strike during a routine dive procedure, the space station plummets into the Geduld, a plasma field that links all the planets like a nervous system and crushes any ship that strays too far into it. With all the adults onboard killed, the young astronauts will have to survive this long journey home in midst of the growing tension amongst each other. Meanwhile the organizers of the sabotage look on and prepare to attack once more.
The deaths during the battle send shockwaves through the Rvyius, as Juli questions whether she should be captain. Friendships are quickly shattered in the wake of the attack on Kozue, as Kouji tries to determine what he wants most.
Yuki takes control of the Vital Guarder, using its' gravity-warping abilities to poke a hole in the Dicastia's gravity-sphere. At the same time, he uses the P.A. system to deliver a scorching verbal smackdown to the Ryvius crew. Once outside the gravity-sphere, the Vital Guarder uses a combination of gravity-warp and the Ryvius' cannons to take down the Dicastia and its' Vital Guarder. Meanwhile, Kouji is unaccountably late returning from an errand. Both Yuki and Ikumi are displeased with him, but they don't know that Kouji had been cornered by Airs Blue, who is still on the Lift Ship. Kouji fails to mention this, for reasons of his own. As the Ryvius approaches Jupiter, Juli is still struggling to function effectively as Captain.
Ikumi Oze is now Captain of the Ryvius, and orders a new ranking system, assigning duties and living quarters according to ability. Disruptions and hard feelings are widespread, especially when the ""E""-class (including Kouji) are locked into their area and the lights are turned off. A ""bubble"" of normal space is discovered at Sere 7, while Kouji finds a way out of ""E""-class. He confronts Ikumi, Yuki & co., but just ends up being shot in the shoulder. Nobody bothers to help him; they just leave him slumped on the deck, bleeding heavily.
Taking control of the Vital Guarder, Ikumi shows how serious he truly is when it comes to his demand of peace. Meanwhile, aboard the Ryvius, Fina takes drastic steps to cut off Kouji's past.
Kouji is rescued, and his friends bind his wound as best they can. The Ryvius enters the normal-space ""bubble"", and discovers that strange, vaguely squid-like creatures dwell within. Scientific study is cut short when an enemy ship, the ""Gespenst"", is detected approaching the ""bubble"". Meanwhile, Criff Cay reluctantly agrees to help Kouji (she's the only one with medical training), and is able to use the equipment in Sickbay to remove all of the needles from Kouji's wound. The Gespenst attacks the Ryvius, causing severe damage and about 20 deaths. The ""Squids"" attack the Gespenst, but it is somehow able to absorb their power. Ikumi orders a retreat, heading up and out of the Gedoult. Once the Ryvius reaches normal space, the bulk of the crew is evacuated to the Lift Ship, but about two dozen people are left behind, including Kouji and the people who've helped him.
All but a few of the crew have been evacuated to the Lift Ship which contains the Vital Guarder. The Ryvius, now powerless and dead in space, is boarded by enemy troops, who are quite surprised to find that there are only children aboard. Ikumi Oze seems to snap under the burden of command. Kouji Aiba and Aoi Hosen must take one last, desperate gamble to save them all.
The survivors of the Ryvius are finally readjusting to life after their epic voyage, when they receive a startling proposal from the Orbital Security Bureau; to return to the Ryvius as its' official crew. Apparently, no-one else has been able to make the ship work since they left. Kouji struggles between his resentment of a government agency that nearly killed him, and his desire to return to the Ryvius.
As the condition of the Liebe Delta Station deteriorates even further, we start to see the intentions of the saboteurs. In an attempt to save everyone aboard the station, the Zwei evacuate everyone into the Rever and ready it to launch out of the Geduld. However, in order to prepare the launch in time, the remaining teachers purge what's left of the station to lower its velocity. In the meantime, Kouji and Ikumi are rushing to the Rever while carrying Faina who was injured duing the panic. They make it back in time as the teachers carry out the purge, sacrificing themselves in the process.
Following the Ryvius' successful battle in Mars orbit, the crew decides to throw a party to celebrate and boost morale. But during the party, a terrible thing is learned by the students aboard the Ryvius.
Thanks to Stein's technical wizardry, the crew has mutinied against Airs Blue & co., leaving Kouji Aiba in a state of confusion. No less confused is Juli Bahana, newly-elected Captain of the Ryvius. Her first attempt at reform, a proposal to scrap the unlimited food-points system for select members of the crew, is unanimously rejected. Juli predicts that it will foster resentment among the crew, and she's right! She agrees to Stein's suggestion that the Ryvius keep going past Saturn, and use probes to contact various colonies and outposts directly; unfortunately, this effort fails, thanks to the Orbital Security Bureau. Next, she asks Kouji to be her liason with the Lift-Ship; this decision backfires, thanks to Yuki Aiba's irrational hatred of his elder brother.
Tensions continue to rise among the crew of the Ryvius as crime increases. As the violence continues to grow, Ikumi is forced to make a choice that will change the landscape of the Ryvius forever.
The Ryvius is an advanced space cruiser of unknown design hidden deep inside the Liebe Delta station. It has a sophisticated computer control system, multiple support craft, a combat mech known as the Vital Guarder, a perfect 1G environment, and enough supplies to last the students for many months. Everyone aboard the Rever, except for the sabotuers, moves into the Ryvius and settle into the ship, expecting a long wait until they are rescued.
Everyone aboard the Ryvius tries to get along while they wait for help. However, they give that up as they realize that the captive saboteurs were with the Orbital Security Department and prepare the ship to move. Elsewhere, the news of Liebe Delta's destruction reaches the public as the OSD ship crew prepare for another fall back plan. The Ryvius' computer system is finally decoded and is ready to use. And just in time as the OSD are littering the Geduld with mines in an attempt to force the Ryvius out. By using the gravity field, the Ryvius manages the fend off the attack and dive even deeper into the Geduld. However, all of the remaining pieces of the central column fell off of the Ryvius, including the Rever which still has the saboteurs.
While preparing to escape the Geduld, the saboteurs try to take over the Rever so they will reach their rendezvous point. However, Aires and his gang foil their plan and the saboteurs are locked up. With the Rever finally ready to launch, the Zwei begin the countdown. In the end, nothing happens and instead of moving out of the Geduld, they are being pulled even deeper by the sabotuers' ship. Suddenly, the Rever regains power, with the help of Neya, and the Rever along with the central column of the station. As the station surfaces, we see that the central column is really a ship called the Ryvius.
While learning how to operate and survive on the Ryvius, the crew aboard the saboteurs' ship prepare for their backup plan. The Zwei assign groups for certain jobs to make the operation of the Ryvius much smoother. However, Kouji and Yuki are placed into the same group and they are less than enthusiastic. Yuki's bitterness towards his brother, though, makes him take his anger on his brother, all while the Ryvius is being attacked. The Ryvius automatically defends itself by creating a well of immense gravity, destroying the ships in the process.
The Vital Guarder manages to fight off the enemy, but takes damage in the process. While the Ryvius heads towards Hyperion, Airs Blue orders the Lift Ship (mostly out of contact with the Ryvius), on the same course. But what he doesn't know is that Stein, on the Ryvius' bridge, is recording every word he says [I said ""mostly"" out of contact, remember?]; an act that will have severe consequences for all of the Ryvius' crew.
A routine dive into the Geduld has turned into a struggle for survival as an act of sabotage sends the Liebe Delta Astronaut Training Center and everyone inside into certain destruction. Things continue to worsen as the station begins to collapse due to the effects of the Geduld. Someone becomes trapped near the collapsed area as Kouji and Ikumi hurry to rescue the person. However, there are dangerous levels of radiation separating them as Yuki, Kouji's younger brother, stops them and turn them back in an unfriendly manner.