Well, I know what you're thinking, Sam. Why did it have to be clowns?
Dean: Planes crash!
Sam: And apparently clowns kill!
Sam and Dean investigate a series of murders that have occurred while a circus is in town. A clown has been seen in the vicinity of the deaths. Dean teases Sam about his fear of clowns: "You still bust out crying whenever you see Ronald McDonald on the television."
The boys start investigating Cooper's Carnival and their suspicions are aroused after a little girl sees a clown her parents can’t see. They stake out the girl’s house, and manage to save her from a clown, who disappears as they shoot at it.
Sam calls Ellen, who tells the boys the creature is a rakshasa that must be killed with a brass dagger. Suspecting Mr. Cooper, the carnival owner, the boys return to the circus. The real culprit is the blind knife thrower, who attacks the boys and traps them in the fun house. Sam manages to kill the rakshasa with a brass pipe from the organ.
That clown chair was not in the script... We did a whole ton of little ad libs to make uneasy, which was fun. For that one, all I did was put a folding chair next to it and did a specific shot to show the clown chair and the regular chair. As the boys came in I said to Jensen "Sam hates clowns, which chair do you sit in?"
Dean comments when examining Andy's van "Not exactly a serial killer's lair, though. There's no... clown paintings on the walls, or scissors stuck in victims' photos. I like the tiger."
When Sam says he's had a weird dream, Dean retorts "Yeah? Clowns or midgets?"
John Wayne Gacy's clown art is mentioned when Dean sees some creepy clown art done by Martin Creaser.
When Ezra Moore first sees Dean in his 2012 outfit she asks "Who's he? Some farmer clown?"
Howard is using hoodoo to exact revenge on people he perceives as mean or neglectful parents. Howard takes a drawing of the child's fear, which the restaurant chain encourages them to do on placemats, and combined with an object owned by the parent. There is power in the child's fear, and combined with the spell, it manifests in reality.
When Sam and Dean arrive in Wichita, Kansas, Sam is reluctant to go to Plucky Pennywhistle's Magical Menagerie and Dean teases him that it's because of his clown phobia. Sam denies it, but is obviously uncomfortable when he is confronted by all the clowns at the restaurant. Another employee, Cliff, tells Dean and Sam he and Saul heard noises coming from the sub-basement. When one of the waitresses Libby berates her son Tyler, she appears to be the next victim. Sam follows, on the lookout for the giant robot with laser beam eyes (Tyler's fear).
Dean goes to the sub basement, and finds Howard's hoodoo books and equipment, including a cauldron with a fire in it. Howard confronts him, and tells him he's put a spell on Sam. As Sam watched Libby and Tyler, he is approached by two evil-looking clowns, who attack him. Dean manages to get a clown statue Howard owns, along with a drawing he did of his brother drowning, and tosses them into the fire. Howard's drowned brother appears, and Howard "drowns." His death causes the clowns attacking Sam to disappear in a shower of glitter.
Afterwards, Dean apologizes to Sam for leaving him at Plucky Pennywhistle's Magic Menagerie when he was a kid, assuming that's where Sam's clown fear comes from. Sam says that fighting the nightmarish clowns was "therapeutic". But when Dean gives him a toy "Plucky Pennywhistle" calling it his "clown phobia sobriety chip," Sam grimaces, and throws it out the window as they drive off.
When Rita Johnson shows Sam and Dean a picture of her brother Chester, he's in a clown costume as he was a children's party performer. Sam grimaces at the sight and quickly pushes the picture away. He later encounters a clown in an elevator of the hospital and is noticeably nervous and uncomfortable around the man. Sam eventually realizes the man is possessed by Chester's ghost after seeing his bloody scalpel and the two fight, ending with Sam expelling the ghost with an iron railroad spike to the man's neck. Dean is disbelieving when Sam tells him the story, but Sam points out that evil clowns are not a joke to him.
Clowns in Popular Culture
An extreme fear of clowns, induced by heavy makeup, nose, and a wig used to conceal the wearer's identity.
Clowns as evil rather than playful have become an established character in popular culture. Notable icons of evil clowns include John Wayne Gacy, a serial killer who killed 33 young men and often appeared at parties as Pogo the Clown, and Pennywise the manifestation of the evil monster in Stephen King's novel (and subsequent movie) It. There are also musical groups such as the Insane Clown Posse.
There are two major reasons clowns have become entrenched as signifiers of horror. One is that a common device in tales of horror is to find make the mundane and ordinary creepy. The more innocent the thing or character usually is the more shocking its transmutation to evil. (see the entry on toys).
Clowns also look human but their true faces are hidden. As is the case with scarecrows, for us the inability to interpret facial expressions provokes fear – think also of horror villains from the Phantom of the Opera to Michael Myers from Halloween or Leatherface from The Texas Chainsaw Massacre movies.
The other reason for clowns being objects of horror is that many of them are actually evil e.g. John Wayne Gacy. There is often suspicion these days around any man who works in a profession that focuses on children, and some clowns have been involved in child abuse.
The evil clown can also be seen as a signifier of a loss of innocence, a sign of the end of childhood. In 2.02 Everybody Loves a Clown Sam and Dean are grieving for their father, trying to cope with the loss of their only parent. It is a time of transition for them; it marks their passage into adulthood. Sam's on-going fear of clowns could be seen as a symbol of his damaged childhood.