Gravitina decides to help Zurg wipe out Star Command.

A rash of stolen technology leads Team Lightyear to discover that XL, the proto-version of XR, has been fixed up by Zurg and sent out to soup himself up and wreak revenge upon Star Command. When Buzz attempts to lure XL into a trap by using XR as bait, Commander Nebula ends up kidnapped, instead.

After an inspection of the planet Rhizome's bio-defenses, Team Lightyear are all given energy plants by Professor Triffid. Booster picks up a red one instead of a white one. The plant is slowly taking over the ship and then Star Command itself. XR has begun to give unauthorized tours for Buzz Lightyear fans behind everyone's backs.

Buzz is impressed by rookie Flash Flemming, much to Booster's chagrin. Gargantia's ambassador Ursona Major contacts Star Command in order to join. But it turns out that there are rebels, who oppose the idea of Gargantia joining Star Command and thus possibly losing their individuality.

Warp Darkmatter hijacks a cargo ship which is carrying NOS-4-A2's coffin and Team Lightyear comes to stop them.

Buzz and Mira are chasing after Lardak for counterfeiting and when they are taking him back to 42, they see Trade World being destroyed. Zurg contacts the Galactic Alliance and tells them to surrender or more planets will be destroyed.

Scientist Ozma Furbanna asks for help to stop the poaching of native animals on the planet Karn. Mistaking him for a rare species, the poachers kidnap Booster.

Warp Darkmatter and Buzz find out that there is an odd implanted device within both of them. So they work together to discover who gave them the implants.

Buzz and XR respond to an emergency distress from Sentilla looking for a downed cargo ship of Hyper Bombs.