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.
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.
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.
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.
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.
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.
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.
The crew aboard the Ryvius must make a difficult decision after the news broadcast. Meanwhile, those back on Earth continue to conspire about the Ryvius.
As tensions rise among the crew over the point system, a new enemy comes forth from space.
When the battle with the Blue Impulse begins, questions and revelations abound as the Impulse releases it's own Vital Guarder. What is the Blue Impulse?
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.
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.
Kouji and Ikumi talk Yuki out of his tantrum and convince him to stay with the Lift Ship. Meanwhile, back on Earth, the guys responsible for this mess are talking things over. The loss of Hyperion is dismissed as a minor concern; more troubling is the fact that the captain of the Blue Impulse ""drill ship"" has had a total nervous breakdown and is now in a padded cell.
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.
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.
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.
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.
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.
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.
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.