From SpongePedia, the First SpongeBob Wiki.
It begins in the Krusty Krab where a man gets a krabby patty, but then a baby comes and takes the Krabby Patty. Everyone thought it was cute, thinking it was a real baby, but Mr. Krabs was able to see Plankton inside the baby. Mr. Krabs started beating him up, but because everyone still thought it was a real baby, they were all outraged. Then Mr. Krabs ripped off the head. Mr. Krabs put the head back on and launched him back to the Chum Bucket and Karen then took off the diaper and put it in the trash where Plankton walks out. Karen told him that he should get a pet and SpongeBob, who just happened to hear their conversation, decided to help him look for a pet. At the animal shelter, Plankton sees a guard worm, an old gross snail, and even Patrick. Plankton almost gets swallowed by a pet. Then, an amoeba saves his life. Plankton chooses the amoeba and decides to call him Spot.
At the Chum Bucket Plankton teaches Spot some tricks like stay, sit, and roll over. Then he teaches him how to steal a Krabby Patty. Plankton wasn't finished talking when Spot left to the Krusty Krab unseen to get a Krabby Patty. When Spot comes back, Plankton is rapt, thinking he finally won but is then enraged when Spot eats the krabby patty in one bite. He punishes Spot by tying his leash to the mailbox. Seconds later, Plankton feels bad, but when he runs back outside he finds Spot's leash, with no amoeba to be seen. Plankton then goes out to find him, with SpongeBob's help. Soon they stumble upon the shelter, then go inside. It is very dark inside so SpongeBob tries to find the light switch. There are 2 switches, so SpongeBob turns on both. One turns on the lights, and the other opened the pens. The guard worm, sea monkey, and sea urchin all chase SpongeBob and Plankton. When they lose the animals,SpongeBob asked Plankton if he has always had a double pupal so Plankton realises Spot had been on his optical cornea (his eye) the whole time. The other pets then find Plankton and SpongeBob again so Spot tries to scare them off. The animals laugh at Spot because he's so small but then he grows about a hundred times bigger and easily scares the animals away. Plankton then decides he is going to keep Spot and was sorry he yelled at him.