The series picks up five years after The Great Tomato War (much as the film Return Of The Killer Tomatoes did), where tomatoes are banned. However that hasn't stopped Dr. Putrid T. Gangreen from engaging in his experiments. Gangreen's ultimate goal is to rule the world and he won't let anyone stop him.
Dr. Gangreen creates a new "Itty bitty cherry tomato" that grows bigger when it eats. Soon giant tomatoes invade San Zucchini is over run and it's up to Chad, Wilbur, Tara and F.T to save the day.
Dr. Gangreen invents a whistle that makes tomatoes attack. Igor and Zoltan kidnap Whitley White and Igor fills in as "Substitute Anchor Man" on Whitley's show. Chad stumbles onto the kidnapping while delivering a pizza and ends up getting kidnapped himself. F.T. and Wilbur soon rescue Chad and Whitley and they quickly hatch a plan to stop Dr. Gangreen from playing his whistle on television.