At the beginning of the film, Buzz Lightyear and Warp Darkmatter were partners as well as best friends, sent by Star Command in order to search for three missing Little Green Men, stumbling upon one of the Zurg Empire's secret bases on an uncharted moon, where the Evil Emperor himself tortured the LGM's for information about their mind link. Though Buzz and Warp succeed in rescuing the LGM's, Zurg escapes, leaving his army of Hornets to attack them and activating his self-destruct sequence on the way out. In the chaos, Warp was pinned under some debris and Buzz attempted to save him, but Warp insisted Buzz to leave without him, pressing a button to force him to escape while he was caught in the explosion, leaving the devastated Buzz to believe that he's dead.
Later, Zurg had gained a new henchman named Agent Z, who leads several Hornets to attack the homeworld of the Little Green Men in order to steal the Uni-Mind, the mystical orb which psychologically connected all LGM-kind. Despite the best efforts of Buzz and his new robot partner, XR, Agent Z bested them with his impressive skills and cybernetic arm which housed a multitude of dangerous weapons, allowing Zurg and his forces to make off with the Uni-Mind in order to use it mentally to enslave the galaxy.
Later, when Buzz invades Planet Z, Agent Z battles Buzz, but Buzz defeats Agent Z and threatens him at a laser point, declaring him under arrest. It was then that Agent Z removes his helmet and reveals himself as Warp Darkmatter, shocking Buzz long enough to allow the latter to knock him unconscious. When Buzz regains consciousness and asks him about his betrayal, Warp reveals that he has been secretly working for Zurg ever since his days at the academy, serving as a spy within Star Command until he had learned the Uni-Mind's existence. Warp also revealed that the previous kidnapping of LGM's and the self-destruction sequence was just nothing but ruses to fake his death in order to sever his ties with Star Command and that he finds the epitome of evil to be more fun and profitable. This leaves Buzz so shocked and furious that he considered Warp as his best friend. Zurg then appeared and began to taunt Buzz on his naive friendship with Darkmatter, and then plans to corrupt the Uni-Mind as well. However, Buzz was rescued by XR and Star Command's janitor, Booster. Zurg then orders Warp to kill Buzz Lightyear but was knocked down by Mira Nova, disguised as a hornet. When XR and Booster crash land, Warp tries to take a shot at them, but Mira ejects Booster out of his ship and onto Darkmatter, pinning him down and bruising his ego.
Warp is then cuffed into a pole and begs help when Zurg's laser begins to detonate. He is then escorted by Booster and XR, becoming scared when they parachute off the building to safety. Meanwhile, Buzz and Mira restore the Uni-Mind by phasing Buzz into it. Warp believes Buzz to be dead at that point, only to be disappointed when he finds out he's still alive, thus foiling Zurg's diabolical plans for conquest. With Zurg's plan foiled, Warp is then taken into custody by Star Command afterward.
- Warp Darkmatter has some similarities with Bucky Barnes, they both have prosthetic arms and are former partners of the main protagonist and were presumed dead. Unlike Bucky, Warp was evil, to begin with.
- Warp Darkmatter shares some similarities with Riley Hicks from Fast & Furious 6, they both used to get along with one of the heroes to Buzz Lightyear and Luke Hobbs respectively. Unlike Riley who is female, while Warp is male and while Riley Hicks is dead, while Warp's fate is left unknown after the events of Ancient Evil.