It begins in that 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 everybody still thought it was a real baby, they were all outraged. Then Mr. Krabs ripped off the head revealing Plankton inside a baby robot. 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, Plankton realizes 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.
There's an episode of Phineas and Ferb called, "Spa Day," that is outwardly similar to this one. In the mentioned episode, the People of Danville were saying "Awww!" which made Doofensmirtz say, "Don't you people have jobs?" which was similar to the People of Bikini Bottom saying "Awww!" and Plankton saying the same thing.
When Plankton takes Spot for a walk, he tires over walking a long distance in comparison to his height. Yet, when he ties Spot to the mailbox post, he does not tire from the walk to and from the mailbox post. In fact, he even makes both the trips in record time for his size.
When Spot multiplies into a large organism, this is through a process of cellular division known as mitosis, where a cell makes a replication, or clone, of itself.
When SpongeBob flips the switch that opens the animal pens, the sea urchin was in the third pen. Then, when Spot scares the animals back into their pens, the sea urchin goes into the second pen. It is possible that they were too scared to get back in their own pens.
When Spot is in the Krusty Krab and SpongeBob opens the kitchen door, for some reason, SpongeBob's mouth moves but no dialogue is heard.
Right as Plankton (who was still in his baby disguise) was about to land in front of the Chum Bucket after being kicked out of the Krusty Krab by Mr. Krabs, the road that usually connects to the Krusty Krab isn't there.