Mika Seido is on her way to her new assignment. She arrives at Maracanan Station. There she meets an old friend, Sofia, who is like a big sister to her. The happiness of their reunion is cut short, however, when Hiroto Amagiwa enters the room. Since he’s a man, he’s heavily guarded. Mika recognizes him as the one responsible for the death of her best friend, Ryoko. She tries to get to him, but she fails due to the high security around him. Mika and Sofia then decide to head to the bar. There they meet two other members of their new team, Tiki and Mario Musicanova, who are brother and sister. Mika is amazed, because siblings are very rare in the genetically engineered society. Elsewhere, Lord Sergei Sneak IV is making preparations. With him is his Register, Sibyl. On the Ring, Mir, arguably the most perfect human in existence, is on a mission. She encounters some rebels who attack the Ring and barely escapes. Through the struggle, there's an explosion that does some damage

Maracanan Station is damaged and falls out of orbit. Will the people on board survive? And, can Mika and the others save the day?

Now that everyone is aboard the Bilkis and the S-Mission has begun. Sergei orders the Ring destroyed. Mika, meanwhile, is selected to pilot the Shaft, with Sofia acting as the backup pilot. It's a dangerous mission, as the Shaft is still very buggy, and no one is really sure how to operate it. Onboard the ship, the squabbling between the debuggers and the operations staff gets out of hand. The other members of the mission, Tiki, Mir, Remmy, and Mario, can only watch and wait. Things start to look even worse when the Ring notices the Shaft and scans it.

When Captain Amagiwa and the others are attacked by a Ring, can Mika and the others defeat it?

The Bilkis has been boarded by a Ring that can copy human form. When it copies an individual, it drains them of blood and leaves them in a comatose state. Once this Ring is discovered, a shipwide search begins. Mika encounters Hiroto and believes that he's the Ring. To prove his identity, he relays details of the incident in which Ryoko died and he survived.

A strange vessel is detected and taken aboard the Bilkis. It turns out to be a space shuttle from 21st century Earth. Three male astronauts are alive inside. The crew of the Bilkis regards them as primitives, little better than Neanderthals, as they come from the time when humanity almost destroyed itself. However, Mika takes pity on them and tries to befriend them, sneaking them around the ship. But the astronauts may prove the fears about them true. They storm the bridge and take it by force!

The Ring that took the astronauts now attacks the Bilkis. Even worse, Beatrice is still unconscious from when the brain shut down from information overload. Hiroto passes out in the middle of the battle, and Mario assumes command of the Bilkis. Mika battles the Ring alone in the Shaft, but Mir suddenly switches positions and takes the main driver's seat. Before she can do anything, though, a script executes. The Shaft performs a new, incredible maneuver that destroys the Ring. Unfortunately, this only leads to the appearance of multiple Rings!

The crew of the Bilkis has been declared traitors by the I.E.O. To make matters worse, the I.E.S.A. fleet is pursuing them. With Captain Amagiwa still unconscious, the role of captain falls upon Mario. Meanwhile, Remmy's true nature is revealed: She's a terrorist working to restore the "natural" order of things. And she's working for Sergei! She announces this to the entire crew of the Bilkis. Mir doesn't take it well. They're both out to destroy the Council of Elders and the I.E.O. But Sergei's plans go even further than that. When she finds out what he really plans, will she turn against him, even at the cost of her own life?

The I.E.S.A. fleet arrives. Mario bargains with the fleet commander, who's an old friend, to buy the ship a little more time. But there's a wild card in the deck. Jean Gadot, who harbors an intense hatred of Mario, decides to take matters into his own hands. He stages an "accident" in which the fleet commander's ship is destroyed. Will his plan succeed?

With little choices left, Mario decides to assassinate Jean. Will his plan work?

Shaken by recent events, the crew struggles on. Tiki blames Mika for Mario's death. Even Beatrice grieves for Mario. Mika is told that Hiroto's chances of recovery are slim. Mir steals the Shaft and goes off to Ganymede to confront Sergei about his betrayal. Mika pursues her, but is unsuccessful in bringing Mir back. So Sofia is sent after both Mir and Mika. Meanwhile, Dolce finally finishes debugging the Shaft. On Niven Base, Mir confronts Sergei, who says he was waiting for her to come and everything is as planned. A new type of Ring appears in space and attacks the Bilkis.

Oberus is closer than originally thought! It's housed on Europa, another of Jupiter's moons. Hiroto wakes from his coma and tells them to scan the surface of Europa. He then gives orders to attack it. Beatrice breaks down and leaves the bridge. Meanwhile, Sergei tells Mir that humanity is nothing more than a "bug" in the universal program. A bug he will eliminate. When Hiroto orders Sofia to use the Shaft, she refuses. So Hiroto uses the Shaft to teleport himself to the surface of Europa with a bomb. Mika sets off to get him back. And Sergei has his own plans to stop Hiroto.

Rings begin to appear around the sun. The rings cover the sun in an attempt to extinguish it, following Oberus' final program. Mir intercepts Mika and they fight, Shaft to Shaft. However, Mika finally wins out and convinces Mir to return to the Bilkis to be with her friends. On the moon below, Sergei lectures Hiroto about how human DNA has too many errors. He says that it cannot be cleansed, so he's going to destroy all humanity. Hiroto fights Sergei, but it's going to take Mika to finally settle the score and humanity's fate.