As the world tries to move on from the Great Tomato War, Wilbur Finletter, celebrated for his brave actions in defeating the insidious forces of killer tomatoes, has turned his newfound fame into a thriving business called Finletter's Pizzeria. This popular establishment serves delicious pizzas, ensuring none of those feared tomatoes make their way into the recipes. Helping him run the pizzeria is his nephew Chad Finletter, who lives with Matt Stevens, a charming ladies' man.
But not everyone is ready to put the past behind them. The villainous Professor Mortimer Gangreen, the mastermind behind the previous chaos of the Great Tomato War, is busy plotting a new scheme. With the help of his loyal sidekick Igor, he devises a nefarious plan to create a new wave of tomato terror. Gangreen is still haunted by his defeat, which was largely due to the terrible song "Puberty Love," and this time, he has an ingenious idea: harnessing the power of music to empower his tomatoes.
By constructing a bizarre device that submerges regular tomatoes in toxic waste before placing them into a transformation chamber paired with a jukebox, Gangreen discovers that he can transform tomatoes into various forms depending on the tune being played. For instance, Michael Jackson’s tracks can produce lookalike clones of the King of Pop, while the Miami Vice theme might give rise to replicas of Don Johnson. Music that is seductive can turn tomatoes into stunning beauties, while rock—his personal favorite—creates an army of tomato soldiers ready to obey his command.
With this new weapon, Gangreen plans to rescue his imprisoned ally Jim Richardson and install him as the President of the United States. To boost his efforts, he invents a captivating female replica named Tara—at first, she serves him loyally. However, as Tara grows disillusioned with Gangreen's cruel treatment of a mutated tomato she nicknames FT (Fuzzy Tomato), she ultimately decides to flee to Finletter’s Pizzeria, where a romantic connection with Chad begins to blossom.
As the story progresses, a pressing financial crisis looms over the production. Characters break the fourth wall, engaging with the audience directly in a desperate attempt to attract funding by promoting various products. One of the suggestions is thrown out by Matt Stevens, who proposes using product placement, leading to humorous and wild demonstrations of consumer goods as they navigate their adventures.
Eventually, Tara makes her home with Chad and Matt, but Igor remains on the hunt. The story takes a turn when Chad, driven by curiosity, follows Igor's trail to Dr. Gangreen’s lair, where he witnesses the bizarre sight of a tomato being transformed into a human. This unsettling discovery sends both Chad and Tara into a panic, and Tara soon finds herself captured by Igor and returned to her sinister creator.
Determined, Chad becomes convinced that a seemingly ordinary tomato he's acquired from the underworld actually holds the spirit of Tara. Meanwhile, Matt seizes the opportunity, persuading Chad to utilize Gangreen's machinery to restore his beloved. Their experiments result in a variety of unexpected creations, including visions of alluring women that catch Matt's interest, yet their ultimate goal—rescuing Tara—remains just out of reach.
In response to their meddling, Dr. Gangreen retaliates by imprisoning Chad and Matt in his dungeon, where they discover Tara, who has so far managed to evade harm. As the three plot their escape, FT messages Wilbur, calling for the heroics he displayed in the first adventure to help save them once more.
As the final showdown approaches, Dr. Gangreen plans to use his transformation chamber with a countdown that threatens to turn Chad and Matt into tomatoes. With Tara still in his clutches, he seeks to execute his villainous blueprints for world domination. Just as hope seems lost, Wilbur and his team arrive, successfully thwarting Gangreen's grim intentions and freeing Chad and Matt from their tomato-bound fate.
The ensuing battle is fierce, with Dr. Gangreen unleashing an army of transformed tomatoes equipped with weaponry, culminating in an intense standoff where Tara is threatened with a gas chamber and only rescued at the last moment by Chad and Matt. Unfortunately, exposure to the gas changes her forever as she retains her human form but is now permanently altered. The townsfolk celebrate their victorious battle against Dr. Gangreen, with FT hailed as a hero for his noble act of sacrifice to save everyone.
In a heartwarming conclusion, Chad and his newly humanized Tara ride off into the sunset, with Wilbur giving his blessing, while Matt revels in the aftermath, surrounded by an array of beauties—all made possible by the demise of the tomato menace and the whimsical adventures they’ve shared.
As the curtain closes on this chapter, a post-credits scene teases a new threat with an army of mutated carrot soldiers, setting the stage for potential chaos yet again.
