RETURN OF THE KILLER TOMATOES!

Ten years after the events of Attack of the Killer Tomatoes (referred to as the "Great Tomato War"), tomatoes have been outlawed, although authorities still deal with "tomato smugglers". Wilbur Finletter has been praised as a hero of the Great Tomato War and parlayed his fame into opening Finletter's Pizzeria, which serves tomato-less pizzas. Working for Wilbur is his nephew Chad Finletter. Chad is roommates with Matt Stevens, a suave ladies' man.

Professor Mortimer Gangreen, the mad scientist responsible for the Tomato War, and his assistant Igor seek to unleash another wave of tomato terror. Gangreen was perplexed at being defeated by "Puberty Love", the worst song ever created, and says that this time music will aid, rather than hinder him. By dipping ordinary tomatoes into vats of toxic waste and placing them into a transformation chamber, Gangreen uses a juke box hooked up to the chamber to create virtually anything based on the song he has picked; Michael Jackson music seems to make tomatoes into a clone of Jackson, the Miami Vice theme makes replicas of Don Johnson, and seductive music turns tomatoes into beautiful women. Gangreen's preferred music is rock, which creates soldiers. With his tomato commandos, Gangreen seeks to break out his imprisoned ally Jim Richardson and install him as President of the United States. Gangreen has also used his device to create an attractive female replica named Tara, who serves Gangreen until she realizes his abusive attitude towards a mutated tomato whom she dubs FT, or Fuzzy Tomato. Tara defects to Finletter's Pizza where she starts dating Chad.

The plot breaks the fourth wall as the characters relate to the audience that the production has run out of money. Matt suggests product placement as a solution. The characters showcase and promote various products as the plot continues.

Tara protects FT while living with Chad and Matt. As Igor searches for Tara, Chad notices his garbage truck and follows it to Dr. Gangreen's house; Chad watches as they transform a tomato into a person. Arriving home, Chad finds Tara consuming plant food—they both scream and she runs away, only to be kidnapped by Igor and returned to Dr. Gangreen. Chad grabs a tomato from a smuggler, believing it to be Tara. He and Matt use Dr. Gangreen's equipment on it. They find the machine can create a wide range of people depending on the music used, including more beautiful women (of great interest to Matt) but they do not get Tara back. They are captured by Dr. Gangreen, who squishes the tomato and has Igor throw them into the dungeon.

There they find Tara unharmed, and she and Chad reconcile. Outside the locked door they hear FT, to whom they pass a message to deliver to Wilbur, who gathers a team of heroes from the first film to rescue the captives. Dr. Gangreen forces Chad and Matt into the transformation chamber and starts a countdown that at the end will transform them into tomatoes. He and Igor leave with a captive Tara to raid the prison and start Dr. Gangreen's plan for world domination; Wilbur and his team rescue Chad and Matt.

At the prison, Dr. Gangreen transforms a bag of tomatoes into a well-armed assault team. While fighting, Gangreen and Igor imprison Tara in a gas chamber and threaten to gas her if the pursuers do not surrender; Igor has a hand grenade. FT throws himself on the live hand grenade before it explodes and Gangreen triggers the gas. As the fumes envelop Tara behind the door she and Chad have a tearful farewell. Matt presses a button to clear the gas from the chamber.

Chad opens the door to find an unharmed Tara. Gangreen plays music to transform Tara back into a tomato but nothing happens; exposure to the gas has made Tara permanently human. After Gangreen and Igor are taken into custody, the town celebrates, and FT is the guest of honor. Chad and Tara ride off into the sunset with the blessing of Wilbur, and Matt dismantles Dr. Gangreen's transformation machine. On a beach, Matt holds a tomato and is surrounded by several buxom bathing beauties.

A post-credits scene shows mutated carrot soldiers with rifles, having killed two humans.

Gangreen's plot is ultimately foiled, and his tomato army is stopped, saving the day for Finletter and friends.

The film concludes with the heroes overcoming Gangreen’s bizarre scheme, underscoring the film’s commitment to parody and absurdity. The ending lands as both a sendup of sci-fi invasions and a wink at its own over-the-top premise, ensuring the tomato threat remains a juicy punchline rather than a real menace.