Zurg gives Torque the cloning device that mostly serves to define Torque's character. Team Lightyear has to deal with him.

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.

XL has found that the primary difference between he and XR is that XR has a component called an AFD, so he kidnaps XR and removes his AFD.

When Buzz is pulled into a black hole, Zurg tricks him into revealing all of his secrets in his latest attempt to destroy Star Command.

Buzz and Mira crash on the distant planet Roswell. Booster and XR have to save them from the local military authorities, aided by the local sheriff and his daughter.

Torque is taken to Penal Colony Seven by Booster and XR; he escapes from them and wrests control of the prison (with the aid of his many ""clones""). At the same time, the President of the Galactic Alliance is being given a tour of PC-7 and being shown its high-tech security system. The security system proves to have some ""bugs"" when it determines that all non-secure persons in PC-7 MUST be escaped prisoners, thus it attempts to capture and subdue not only Torque (and his ""clones""), but also the Galactic President, Booster, and XR. From orbit outside PC-7, Mira and Buzz attempt to help out, but the system interprets their actions as aid for the supposed ""prison break"" going on inside.

Compu-klerm Co. brainwashes Buzz into thinking that he is an office clerk. Buzz's combat skills are downloaded into the Klerm Slambots, which Team Lightyear then have to fight to save Buzz.

Tangean noble Lord Angstrom tries to get Mira to wed Fop Doppler, a fairly minor member of the Tangean noble clique (and fairly snooty) so as to provide a distraction as a band of Tangean ""Grounders"" attack and allow for Lord Angstrom to overthrow Mira's father. The Grounders are a humanoid race that shares the planet Tangea with the race that Mira is native to. While the blue-skinned, svelte, and fairly bourgeois Tangeans (""Tangean Blue-bloods"") have the psychic ability to phase through solid objects (...aka...""ghosting""...), the taupe-skinned, stocky, and fairly proletarian Tangeans (""Tangean Grounders"") have the psychic ability to project focused force-blasts (...aka...""boom-boom""...). For some reason, the native psychic abilities of both Tangean races are nullified if either race is in close proximity to the other. In hopes of avoiding marriage, Mira invokes a law requiring Fop to submit to a ""Challenge of Worth"". She selects Ranger Academy basic training

The crystals for Crystallic Fusion Generators (the primary power source for almost all Galactic Alliance technology) are mined on the landless ocean planet Bathyos; an anti-air breather movement, hoping to cause an embargo that will force the Galactic Alliance to bow to the will of the Bathyosians, is lead by Gularis, a shark-esque big-wig native of Bathyos. The movement is taking terrorist actions, causing ""accidents"" to happen in the crystal mines, but Team Lightyear is called in as a safety measure, and they uncover Gularis' plans.

One of Zurg's Brain Pods (Number 13) goes AWOL, so Zurg hires the Boba Fett-esque bounty hunter Shiv Katall to track him down; Buzz turns out to've been Shiv all this time, in order to make defectors from Planet Z seem to be dead, when they're really in a witness relocation program; Buzz gets found out, so Commander Nebula has to do the Shiv-thing (...which he USED to do, before Buzz came along...), in order to make Zurg regain trust in the existence of Shiv Katall.

Mira, Booster, and XR are all nominated for the Rookie of the Year award. The three compete with each other to impress Buzz, which Zurg uses to steal a new matter transporter.

Buzz captures ""Pen-like Activation Device"" for Zurg's HYPER-DEATH RAY in a fairly accidental manner (Buzz thinks that it MUST be important and just LOOKS like a pen...everyone else thinks that it MUST be just a pen and that Buzz LOOKS to be going a little loopy...); Buzz is sent to Rhizome to work out overworking-stress with Tubunch. Zurg goes to Rhizome to get a clear shot at Star Command with his HYPER-DEATH RAY, unaware that Buzz is there. Buzz channels his emotions and uses the Rhizome plant-tech to stop Zurg.

Chlorms (Epoch, Era, & Eon) kidnap Galactic Alliance senators for zoo exhibits. Team Lightyear gets nabbed, but Buzz attempts to rescue them. They all end up shipped to product testing due to a lack of co-operation. They escape and return to Star Command

Zurg mutates Jo-Ad vegetables w/ Transdibulator. Team Lightyear goes to Jo-Ad to investigate the problem. Booster's childhood pal, Buster, was lured into helping Zurg w/ the promise of glory and power (he had been jealous of Booster getting to join Star Command while he was stuck back home on the farm).

Mira ghosts into a Crystallic Fusion Generator Core and becomes a glowing, supercharged, power-speed-junkie. Mira's father warns Mira about how her race can fall prey to such temptation, but Mira has to find out on her own. Eventually, after she attempts to battle Zurg on her own, she realizes that her need for ""re-charging"" is getting worse and worse and is beginning to take control of her life, but she manages to overcome her ""energy addiction"".

XR downloads Star Command Mainframe to prevent the system from crashing (due to Warp Darkmatter using info-stealing techno-ticks); Zurg heists XR in order to gain Star Command classified information; XR uses techno-ticks to help HIM out.

Petra, a senator's daughter, is shipped off to Space Ranger Academy to keep her from Plasma Boy; Booster falls for her; both Petra and Plasma Boy end up in Space Academy.