Following the events of Monsters vs. Aliens: Mutant Pumpkins from Outer Space B.O.B., The Missing Link and Dr. Cockroach discover a Zombie Carrot in the Murphy's yard created by the remains of the Mutant Pumpkins. They also discover that the Carrot can infect people with a zombie-esque mind control virus by biting them (when Carl Murphy is bitten) and that they multiply when destroyed.
Dr. Cockroach and B.O.B. are forced to retreat into the Murphy house when The Missing Link is infected only to discover that one of the Carrots sneaked in with them. When the carrot bites B.O.B. but is not infected Dr. Cockroach realizes that he's immune since he doesn't have a brain. To this end Dr. Cockroach states that the only way to defeat the carrots and free their loved ones is for B.O.B. to eat all of the carrots.
Unfortunately it's revealed that B.O.B. is deeply terrified of Carrots: during his infancy General Monger force fed him a excessive amount of Carrot Puree that deeply scarred him for life. Refusing to eat the Carrots even after Dr. Cockroach is infected B.O.B. instead makes "new friends" from several stuffed animals and attempts to retreat. However he has a change of heart when he see's his loved ones suffering and decides to "eat his vegetables."
Tearing through the house B.O.B. eats carrots until the point that he's morbidly obese and immobile, leaving only one left that he cannot reach. B.O.B. subsequently develops the will power to reach out and eat the carrot when he sees him opening the last Nutter Buddy Butter Bar freeing all of the carrots victims. In the final scene of the short B.O.B., who has been narrating the story, transforms into a giant Zombie Carrot.