Zurg accidentally stumbles into a parallel universe, where an evil Buzz Lightyear rules. Zurg uses this to his advantage in finally capturing the real Buzz, leaving Buzz to experience the terrors of the parallel world, and Zurg free to destroy Star Command.
Zurg is thinking up his latest plan for taking down Star Command when he discovers one of his Brain Pods had managed to stumble upon a parallel universe where the Buzz Lightyear there is evil to the core and actually had conquered the universe there. Allying with him, Zurg prepares to have the Evil Buzz help him conquer his own universe with the first objective being to take out the good Buzz.
The Evil Buzz travels to the planet where Buzz's house is, and ambushes him when he comes to answer his front door while hosting a barbecue in the backyard that many Space Rangers are attending, using a weapon that vaporizes Buzz's house, leaving only a smoldering crater. Commander Nebula mistakes it as thinking the grill malfunctioned as he had been talking to Buzz about it earlier before he went to get the door, leaving Nebula to handle the grill. As Nebula and Team Lightyear mourn Buzz's apparent death, Buzz wakes up in the Evil Buzz's universe, where he is soon assaulted by the parallel Mira Nova and Booster, both seeking revenge for the Evil Buzz's conquest of their home planets. After taking down a large Hornet that attacks them, Buzz is confronted by the parallel Mira, who intends to kill him as vengeance for the cold-blooded murder of her father, King Nova. Just as she fires, Buzz is rescued by the parallel XR and Commander Nebula, who have Mira and Booster stand down, realizing Buzz might be their only hope of saving both their own and his universe from the Evil Buzz.
Meanwhile, the Evil Buzz and Zurg launch a full-scale attack on Star Command. When the Evil Buzz makes his move to take down Star Command, he is mistaken by Nebula to be the good Buzz and tells the Space Rangers to hold their fire, allowing the Evil Buzz to severely damage Star Command and allow it to be captured by Zurg's Dreadnought. When Team Lightyear catch the Evil Buzz, they mistake him for the good one and try to bring him back to his senses before the real Buzz arrives with the parallel Mira, Booster, and XR to stop Zurg and the Evil Buzz. XR initially fears that if the two versions of Team Lightyear make physical contact, it could destroy the very fabric of the universe, but when Booster moves to save his parallel self, nothing happens, leaving XR to realize he panicked for nothing before joining his own parallel self in fighting off the Hornets.
Taking drastic actions, the Evil Buzz activates the self-destruct on Zurg's Dreadnought, forcing Zurg to abandon ship squelched in an escape pod with all his Grubs and Brain Pods. While Buzz goes to face his evil counterpart, the pairs of Mira, XR, and Booster go to free the crippled Star Command before it can be destroyed with the Dreadnought. After a tough fight, Buzz tries to reason with his evil self, but Evil Buzz shows he is too far gone to be reasoned with, before throwing Buzz in an escape pod and jettisoning him from the Dreadnought, sparing him as Evil Buzz intends to go down with the ship. Team Lightyear and their parallel counterparts are able to free Star Command and then fly clear before the Dreadnought is destroyed in a tremendous explosion.
Back aboard Star Command, Commander Nebula and Team Lightyear share a final goodbye with their parallel selves before the parallel Commander Nebula and Team Lightyear depart to return home with fresh supplies to give them a fighting chance of reclaiming their universe, especially with the belief that the Evil Buzz is gone for good, having perished in the explosion of Zurg's Dreadnought.
However, out in space, Evil Buzz reveals he's still very much alive.