A pair of comets code-named Janus are on a collision course for the Academy, but when the Blue Team investigates, they discover that the closest comet is actually a sentient being named Irgo. The comet is dying, and came to warn sentient beings about the other comet, a criminal named Targ. Can the Blue Team revive Irgo and defeat Targ?
Proteus IX-B, an asteroid that once housed a small mining colony, is about to be demolished. But the appearance of a phantom planet around it leads Blue Team to perform a seance, in which Chris and Laura communicate with a ghostly member of a long-dead civilization, and learn they have to perform a dangerous rescue.
Tee Gar invents a new device known as the "cryotron", which can instantly freeze things. Against orders, he takes it to the planet Delius to test it further, unaware that the frozen things he tested at the Academy have since exploded. When a giant named Dramon gains control over the cryotron and freezes Peepo. The Blue Team may not be able to save their robotic friend.
Despite the fact that he is under investigation for safety violations, Cadet Matt Prentiss is placed in charge of a mission to Asteroid BX-3 to contain a leaking reactor that threatens a nearby colony on Alopek. Blue Team goes with Prentiss - including among them Chris Gentry, who can't stand the headstrong leader - but Prentiss' actions soon put them all in danger.
Paul and Chris are trapped in the Alderan Triangle, then pushed back out into normal space by an entity that warns them away. But Gampu leads the others into the Triangle, they find the millennium-old Starship Hope, a near-duplicate of Space Academy. Aboard it is the aged Captain Rampo, and he has a warning...
Gampu's cantankerous technology-phobic brother visits the Academy. Unfortunately, Sunseed and many Academy crew members are affected by genetically-altered food that Paul has grown on a space farm. The hallucinations and bizarre behavior the food causes results in a deadly situation for Sunseed, unless he can work with Peepo, a being he truly despises.
Interviews with cast and crew made for the DVD release.