A baby appears at a mans table, and the man gives the baby a patty. Mr. Krabs' Plankton Alert alarm then goes off, and looks through a telescope, seeing Plankton in a baby disguise. Mr. Krabs then battles and tries to rip off Plankton's baby disguise while everyone believes it's a real baby. Everyone, including SpongeBob, tell Mr. Krabs to stop, but Mr. Krabs refused. Once the head is off, Mr. Krabs announces that it was just Plankton. He then tosses him out. Plankton tells Karen that he needs something to take his mind off the formula, Karen suggests a pet except she suggests it in a scientific way. SpongeBob surprises Plankton by appearing in the window. SpongeBob and Plankton go to the shelter where Plankton looks at the pets, where in one cage Patrick appears. Then Plankton finds a rock like creature who, once he passes, tries to eat him. An amoeba then runs on the screen, barking, and saves Plankton. Plankton finds that the amoeba is the perfect pet.
SpongeBob then suggests the name Spot, which the amoeba bites SpongeBob. Plankton decides that he should name his new pet Spot since it provoked rage, and then it cuts to the Chum Bucket. Inside the Chum Bucket, Plankton is teaching Spot tricks and discipline. Something Plankton teaches Spot is to steal the Krabby Patty but Spot goes off on his own and brings back a Krabby Patty unseen. Shortly after Spot brings back a Krabby Patty, he eats it and Plankton says Spot is a "Bad Amoeba" and ties Spot to the mailbox. Plankton only leaves Spot outside for about 1 second before he goes out to ask forgiveness from Spot but Spot isn't there. So at night SpongeBob and Plankton have Lost Pet signs, but when that fails they go to the shelter. SpongeBob tries to turn on the lights but before that he opens the cages on accident. Plankton asks SpongeBob what the first switch did and SpongeBob said it opened the cages. SpongeBob and Plankton then run from the vicious animals before they hit a dead end.
SpongeBob then asks Plankton if he always had a "Double Pupil." Plankton then rips off Spot from his eye. They almost get killed but Spot protects them by growing huge until he scares the animals back into the pens. The episode ends with Spot licking Plankton on the face.