Admiral Collins, a Starfleet officer serving the United Federation of Planets, plans to start a war with the Romulans. So he finds Kron's ship and revives Kron from suspended animation. Admiral Collins has Kron create new weapons for a war between the United Federation of Planets and the Romulan Star Empire, including the warship USS Harbinger.
The Autobots rush out to meet a Decepticon sneak attack on their headquarters, unaware that it's actually a diversion. While they're occupied, Megatron and Starscream coat themselves in a temporary "invisibility spray" and sneak inside. Megatron sabotages the Autobots' recharging chamber with a personality destabilizer device, before calling off the attack, leaving the Autobots bemused. After the Autobots recharge the next day, Teletraan I alerts them to the imminent launch of a rocket, and rather than protect it, they want to destroy it. Optimus Prime obeys Megatron's first order and smashes Teletraan I.
Bumblebee, Jazz, Spike and Sparkplug find a spot in the middle of nowhere for Jazz to try out his new sound system. Bumblebee leaves them to it, heading back to Headquarters. Bumblebee makes it back first, and finds Teletraan disabled and Bluestreak behaving oddly. Bluestreak forces him into the recharging chamber, but Jazz arrives in time to discover something's wrong. Jazz manages to disable Bluestreak. Sparkplug repairs Teletraan I, who tells them that the rest of the Autobots are now evil and have now become the Autocons!
Meanwhile, Optimus leads the Autocons on an attack at the local Air Force base, where they begin trashing military jets. Spike and Bumblebee rush off to the base to stop them, and Sparkplug and Jazz stay behind to work on a cure. Hound and Ratchet, on Megatron's orders, have gone after the plans for the human solar energy satellite being launched on the rocket. They start chasing the satellite's inventor, Doctor Harding. Bumblebee reaches the Air Force base, but is unable to persuade Optimus to stop his rampage. Meanwhile the Decepticons take over the rocket base and plan to take the rocket and satellite back to Cybertron.
As this was happening, Kron launches an attack on a Starfleet base in London, killing many Starfleet personnel. In response, Admiral Collins calls the USS New York NCC-2614 back to Earth. He then convenes a meeting at Starfleet Headquarters to discuss a manhunt for Kron. Kron shows up in a jumpship and attacks the meeting, killing Admiral Rogers and other Starfleet officers. Captain Christopher Michaels destroys the jumpship, but Kron uses transwarp beaming to beam himself to Romulus. Captain Michaels receives special permission from Admiral Collins to hunt down Kron. Admiral Collins delivers 210 prototype photon torpedoes to the USS New York and orders Captain Michaels to fire them at Kron's location once he is found. The Guardian Warriors come aboard the USS New York and the Red Guardian Warrior convinces Captain Michaels to capture rather than kill Kron.
The USS New York arrives at Romulus. Captain Michaels and an away team beam down to Romulus, where they are ambushed by Romulans. Kron then arrives and kills the Romulans, then surrenders to the away team. Captain Michaels and the away team return to the New York with Kron as their prisoner and warp to Earth so that Kron can stand trial. Meanhwile, Admiral Collins, aboard the USS Harbinger, beams the Autocons and their Decepticon allies aboard, as well as the rocket and satellite. The Harbinger then lies in wait for the New York.
The New York arrives in the Sol system, where she is confronted by the USS Harbinger. Admiral Collins demands that Captain Michaels hand over Kron. Captain Michaels refuses. The New York goes to Red Alert, raises her shields, and arms her weapons. A battle begins. During the battle, the USS Lexington NX-85453, commanded by Good Vader, arrives to help the New York. The New York is damaged in the battle. The Harbinger prepares to finish off the New York, but suffers a power outage caused by the teenage girl with the pink electric guitar, who had boarded the Harbinger. Knowing that Kron was the designer of the Harbinger, Captain Michaels and the Guardian Warriors ally themselves with Kron to defeat Admiral Collins. Meeting up with the teenage girl, they take control of the bridge. Kron betrays Captain Michaels and the Guardian Warriors and kills Admiral Collins, taking control of the Harbinger. Kron negotiates with Good Vader, who agrees to give Kron the 210 torpedoes. The torpedoes are armed and beamed over to the Harbinger while Captain Michaels, the Guardian Warriors, and the teenage girl beam back to the New York. The torpedoes detonate and the Harbinger crashes into San Francisco, killing all hands aboard, including Kron. Bad Vader, the Emperor of Evil, is furious that Good Vader has foiled his evil plans once again.
Back at the Fun Place, the Guardian Warriors and the teenage girl talk about their adventure. Then the teenage girl goes up on stage with her band and plays some rock music for the Guardian Warriors. The teenage girl plays her electric guitar and sings. The Guardian Warriors clap and cheer as the teenage girl and her band play.