Doctor Aaron's Adventures of Buzz Lightyear of Star Command: The Adventure Begins

As a framing device, Andy's toys watch a VHS copy of Doctor Aaron's Adventures of Buzz Lightyear of Star Command: The Adventure Begins.

Buzz Lightyear (voiced by Tim Allen) and Warp Darkmatter (voiced by Diedrich Bader) are searching for three missing Little Green Men (L.G.M.) (voiced by Patrick Warburton), a noosphere-dwelling race serving as Star Command's Universe Protection Unit's scientists. They discover the lost L.G.M. in a hidden outpost belonging to Evil Emperor Zurg (voiced by Wayne Knight). Zurg tortures the L.G.M. when Buzz and Warp break in; a battle breaks out with Zurg's robots while he escapes. The self-destruct sequence starts, leaving Buzz and Warp a minute to escape. Warp gets pinned under wreckage and forces Buzz to leave just before the explosion happens, presumably killing Warp.

Ashamed, Buzz refuses a new partner, but is given a Star Command recruit, actually Princess Mira Nova (voiced by Nicole Sullivan), who Commander Nebula (voiced by Adam Carolla) trains. With the power of "ghosting", Nova is nearly invulnerable. Buzz reiterates his refusal to endanger another partner, despite Nebula's forceful assertion Buzz isn't to work alone. Buzz later rescues a shy janitor named Booster (voiced by Stephen Furst) from being fired.

In Zurg's fortress, his new second-in-command, Agent Z (also voiced by Diedrich Bader), is given a robotic arm that becomes a variety of weapons. Zurg learns of a huge orb on the L.G.M. homeworld called the Uni-Mind, responsible for the telepathic link between them; he sends his robots to capture it. The L.G.M., after building a robot soldier called XR (voiced by Larry Miller), who is offered to Buzz as a partner as he can be repaired after any damage and can learn from him, get a telepathic message about Zurg's attack. When Buzz and XR arrive on the L.G.M. planet, they are confronted by Agent Z, who destroys XR while the Uni-Mind is stolen by Zurg. Unable to think clearly, the L.G.M. rebuild XR, but with a mind of his own. Commander Nebula decides to launch a full-scale assault on Planet Z, but Mira says a solo ranger could go to stop Zurg with the prototype Alpha-One. Nebula dismisses the idea, deciding to launch the full-scale assault.

Zurg corrupts the Uni-Mind, so he can use it to control minds, while his scientists start making a "Mega-Ray" to use the corrupted Uni-Mind to bend entire populations of people to Zurg's will. Mira and Buzz each attempt to steal the Alpha-One prototype spacecraft; Mira wins and leaves with it. Buzz pursues Mira in his own craft, not realizing Booster and XR are inside it, having entered it to play make-believe. Eventually, Buzz catches Mira and stores Alpha-One in his spaceship's cargo bay; Booster and XR are discovered also. Zurg's Mega-Ray subverts several planets in quick succession such as Rizone and Batheous. He then turns it on Star Command, enjoying the irony of watching his greatest enemies become his mouthpieces. Buzz, Mira, Booster, and XR see the Mega-Ray's beam strike Star Command, and enter it to discover its effects. They discover all of the staff have been suborned by Zurg; they flee in Buzz's Star Cruiser. Zurg uses Star Command's entire arsenal, planting a bomb on Buzz's ship. Buzz and the others escape in the Alpha-One just before the bomb detonates, destroying the cruiser. Not knowing Buzz has escaped the bomb blast, Zurg believes he is actually dead and moves on.

Booster accidentally causes the ship to crash-land on Planet Z. There, Buzz insists on finishing the mission alone. When they start to argue over something ridiculous, Buzz orders them to leave. Buzz fights Agent Z, but he is shocked when Agent Z removes his helmet, revealing himself as Warp Darkmatter. Taking advantage of Buzz's momentary confusion at this, Warp knocks him out and delivers him to Zurg. Warp explains that not only had he faked his death at the beginning of the film, but was secretly working for Zurg for years as a double agent. When Zurg mocks Buzz, Buzz responds by dictating his "final log entry". Zurg and Warp watch in amusement, but Mira, Booster and XR hear Buzz's surrender and his final entry (which includes a coded plead for help). Zurg plans to use the "Mega-ray" on Buzz, but XR and Booster arrive in time to rescue him as it fires. Booster and Mira destroy Warp's mechanical arm after Booster lands on him. Buzz and Zurg face each other; Zurg thinks he has won, but Buzz and his three friends surround Zurg and pronounce him under arrest; but Zurg escapes through a distraction. Zurg triumphantly declares if Buzz goes to any planet, he can hear his voice mocking him. Booster and XR capture Warp and leap from Zurg's now-exploding tower. Mira uses her "ghosting" power to take Buzz to the core of the Uni-Mind. In moments the Uni-Mind is restored to normal, freeing the suborned peoples and leaving Zurg momentarily helpless. The unity of the L.G.M. is restored and Warp is arrested.

The film ends with Buzz, having at last admitted that he cannot work alone, creating a new team called "Team Lightyear" with XR, Mira and Booster (all newly decorated with Star Command's highest commendation). They fly to the galaxy and shout "TO INFINITY AND BEYOND!".