When Marge takes the family to the Family Fun Center, she notices Nelson knocking Milhouse off the track and wins a BB gun from stolen prize tickets. Bart and Nelson attempt to be friends, but Marge refuses to let Bart hang out with Nelson. Bart goes to Nelson’s house anyway and starts using Nelson's new BB gun. When Nelson pressures Bart to shoot a bird in a nest, Bart accidentally kills the bird. Marge is disappointed that Bart killed an animal, but instead of punishing him, she does not have anything to do with his destructive ways.
After Marge leaves Bart with Nelson, Bart discovers two eggs in a bird's nest. Since he does not want the babies to die like their mother, he decides to hatch the eggs, and secretly keeps the eggs warm in his treehouse. After Bart spends more time in his treehouse, Marge starts to suspect he is up to something. After Marge finds out what Bart has been doing, she becomes proud of him. With Marge's help, the eggs eventually hatch, but the Simpson family is shocked when instead of birds, a pair of lizards emerge from the eggs, who Bart names Chirpy Boy and Bart Jr.
Bart and Marge take the lizards to the Springfield Birdwatching Society. Principal Skinner, a member of the society, explains that they are Bolivian tree lizards, a type of lizard that steals a bird’s eggs and leaves their own eggs to be watched after by the mother bird, which is then eaten by the offspring once they hatch. Skinner says the lizards must be killed by law, because they have killed many bird species. Bart escapes and runs away with the lizards, but before he can get away, Skinner catches up to him and they both struggle on top of the building. Suddenly, the lizards glide to the ground, they escape and eventually reproduce and start to eradicate pigeons in Springfield.
Since the town considered the pigeons to be a nuisance, they are delighted that the lizards have eaten all the pigeons. So, Bart is thanked and honored by Mayor Quimby with a loganberry scented candle. Lisa worries the town will now become infested by lizards rather than the pigeons, but Skinner assures her they will send in "wave after wave of" Chinese needle snakes, then snake-eating gorillas, and then "when wintertime rolls around, the gorillas simply freeze to death."