Pilot is the very first episode in the first season of Malcolm in the Middle.
Malcolm is transferred into the accelerated learning class and has to learn to deal with it.
Malcolm introduces himself and his family to the viewers. Downstairs at the breakfast table Malcolm, Reese, and Dewey fight over the remaining waffles while Lois shaves Hal's body hair in the kitchen. Malcolm learns that he will have to spend the afternoon with Stevie Kenarban, a handicapped asthmatic who happens to be in the Krelboyne class (the high honors class). He isn't too pleased.
As the boys are walking to school, Malcolm and Dewey find the bully of the school, Dave Spath, beating up a kid and forcing him to do embarrassing things. Malcolm and Dewey are able to pass by with him seeing them.
We move to Malcolm's classroom in school. The class is painting pictures. When he takes his finished work up to the teacher, she is very impressed with it. While he is talking to the teacher the bully, Dave, places red paint on his chair. When Malcolm sits down there is an audible squish. As we see him walking down the hall toward the office we can hear the laughter of the students.
It turns out Malcolm was summoned there by Caroline Miller, the Krelboynes' teacher, because of his astounding skills. Further investigation shows that he can pass a 'What's Wrong With This Picture' test at extraordinary speed.
When he arrives at Stevie's house that afternoon, he realizes that his parents are overprotective and won't even let him watch television. But they soon find common ground in comic books, and Malcolm thinks that the friendship won't be so bad after all.
The following Saturday, as Lois is getting ready for work and trying to find her bra, there is a knock at the door and none of the boys move to answer it. Lois opens the door topless and finds Caroline Miller outside. Caroline tells Lois that she has not returned any of her calls and is desperate to talk to her about Malcolm. Lois thinks that the counsellor wants to put Malcolm in a special ed class, and informs her that she would never allow it. A dishevelled Caroline explains that she is mistaken and asks to come in and tell her more.
At dinner, Lois announces Malcolm's outstanding IQ of 165, meaning that he will have to join Stevie in the Krelboyne class. The news baffles everyone at the table and Malcolm is more than just annoyed at the notion. He knows that he will be ridiculed for the rest of his life.
Malcolm reluctantly accepts his fate in the class. At school, his teacher brags about him being highly gifted. Later he finds himself with the other geniuses. He accidentally insults Stevie and regrets it immediately afterwards.
Malcolm decides to make up with him, but Dave Spath appears again. He insults the bully, causing him to get up and approach Malcolm. As he nears, Malcolm throws a punch and misses. Then he throws chocolate moose in his face. As the bully winds his fist up, Malcolm ducks. Spath tried to redirect his punch, but ended up slightly tapping Stevie's cheek with his knuckle. Stevie realizes what he can do with this opportunity, waits a beat, and pushes himself over, complaining about the pain. Malcolm and Stevie smile at each other. The crowd surrounding them and even Dave’s own gang rant about his beating of a crippled boy. Nobody believes Dave when he says it was an accident.