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.

Zurg nabs an exhibit of an extinct species of large, Alien (as per the movies)-esque insects, planning to resurrect the species in order to help him in (...what else...) take over the galaxy. Dr. Ozma Furbanna is roped into helping Zurg revive Alien-style bugs, by having her scientific morals preyed upon. Zurg sics the bugs on Capital Planet. Before things can get too out of hand, Team Lightyear discovers that the bugs can be stopped by belly-tickling (...it over-rides their nervous system...), and with that they manage to save the day.

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.

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.

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.

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

Gravitina decides to help Zurg wipe out Star Command.

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.

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

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.

Star Command receives an urgent call for help. Unfortunately the signal was too weak to locate.

When Brain Pod #57 defects to Star Command, Zurg hires Romac, a Tangean Grounder bounty hunter -- and Mira's ex-boyfriend -- to bring him in.

While Team Lightyear is conducting mock-combat training with Team Rocket (...headed by Rocket Crocket...), Crocket goads Mira into getting herself tagged. King Nova presents Mira with an invention of his, the Starthought; a small spacecraft guided by one's thoughts. Mira has doubts about it until she realizes that it'd really bother Crocket to see her zipping around in such a spiffy ship. While testing the Starthought, Mira runs into some tourists, who are actually Warp Darkmatter, along with one of Zurg's Brain Pods & a Grub, on a reconnaissance mission to scope out any new Star Command developments. Zurg sets up a fake raid on a Gulgarian mining outpost, in order to lure Mira, and the Starthought, into his clutches. After successfully losing the Starthought to Zurg (...success for Zurg, dismal failure for Mira...), Mira goes to Cosmo's Diner to sulk, but Team Lightyear & King Nova show up and convince Mira to go out and re-nab the Starthought back from Zurg. They sneak into Zurg

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

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.

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.

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.

Team Lightyear receives a call from Jo-Ad while in the early phase of an investigative mission (involving a series of thefts); Booster's family is letting Booster know that the bunzel harvest (the primary crop on Jo-Ad, which resembles eggplant) is due. When Booster claims that his duty to the Space Rangers supersedes his farming history, his Grandfather reminds him of the legendary ""Bunzel Fever"", that strikes down any native of Jo-Ad that isn't involved in the bunzel harvest. Booster dismisses the legend and eschews the harvest. When it turns out that the legend isn't a myth, Booster goes through a ""pon-far""-type thing, that is marked by him ""hulking out"" into a large, bellicose form that is determined to harvest bunzels, or anything bunzel-esque (...and since this transformation is also marked by him having spells of mistaking anything roughly ovoid for a bunzel, this gets fairly hazardous for anyone who is rotund and/or in a space ranger suit, XR, and Team Lightyear's ship

Answering a distress call, Team Lightyear discovers a ship under attack by Vulturans (a vaguely bird-like race, that XR recognizes as a race that tends to have a thing against robots). Team Lightyear fights them off...but in the battle, XR flies into a mad rage (gets a little ""blowie-uppy"") and ends up being seriously disassembled. When the LGMs fix him up, they discover signs of metal fatigue. Their report is sent to Commander Nebula, who accidentally spills coffee on the report, smudging the lettering and making it look like ""mental fatigue"". XR is sent off to the resort world of Mahamba 6 for a weekend pass, before having to take a psychiatric evaluation from Star Command's resident psychiatrist, Dr. Animus (...who resembles a native of Binpinardia...). While on Mahamba 6, XR is picked up by a taxi driver who turns out to be XL (...he sent XR a fake ""you have just won a free vacation!!""-flier to XR to lure him in...). XL kidnaps XR and steals his body.

Zurg tries to take over the planet Roswell, in order to set up a partner planet to Planet Z. Becky contacts Booster, and Team Lightyear shows up to defeat Zurg and save the day. The climactic battle between Zurg and Buzz takes place in the reactor chamber that is powering his self-constructing re-formation of Roswell; when they begin fencing with glowing reactor rods, and when Zurg attempts to throw Buzz off guard by claiming to be his father, the Star Wars references fly fast and furious. The self-constructing machine is thrown into reverse, Roswell is saved, and Zurg is defeated.

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.

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.

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.