As the Marsh family colors eggs for Easter, Stan questions what it has to do with Jesus. Not satisfied by his father's vague response, Stan storms off and makes the same inquiry to a mall Easter Bunny, who has previously received death threats from a falsely cheery Cartman. The mall bunny tells Stan that it is "just Easter", and to "just go with it", then makes a mysterious phone call.
Stan soon finds himself being chased by men in bunny suits. When he gets home, he finds that his father is part of the plot. Randy calls the men off, and tells Stan that he is in a society called "The Hare Club for Men", who have guarded the secret of Easter for generations.
Randy takes Stan to the headquarters of the Hare Club, where he is to be initiated into the group, which reveres a rabbit named Snowball. Just as he is about to learn the secret of Easter, Stan's initiation is interrupted as the club is ambushed by a group of ninjas.
The Hare Club members rush to protect Snowball, and Randy gives the rabbit to Stan, telling him to run. He escapes with Snowball, and witnesses the ninjas and their leader, William Anthony Donohue, executing a resisting hare and interrogating Randy.
Stan runs off to Kyle's house and tries to extract any knowledge Kyle has of Easter. Kyle, who is Jewish and does not know anything about Easter and was busy finger painting, does not want to be involved in something so dangerous, but Stan persuades him to help.
Stan and Kyle manage to track down a man named Professor Teabag (spoof of Professor Teabing), who supposedly knows the secret of the Hare Club. Teabag lets them in his mansion and explains that Leonardo da Vinci was actually a member of the Hare Club and that Saint Peter was not a man, but a rabbit (Peter Rabbit), and that laser imaging shows that da Vinci originally portrayed Saint Peter as a rabbit instead of as a man in his painting of the Last Supper.
Teabag explains that Jesus knew that no human could speak for all Christianity without any acts of corruption, and that rabbits were pure, tolerant, and incorruptible. This is why the Pope's mitre is shaped to accommodate a rabbit's ears.
He also explained that the Catholic Church decided to bury the secret and put a man in charge, ever since, "The Hare Club for Men" society members have decorated eggs for generations to keep the secret in da Vinci's painting alive.
He further explains that Snowball is actually a direct descendant from St. Peter, and that Stan's father and the members of the Hare Club have been kidnapped by the Vatican, who wish to cover up this secret, thinking of it as blasphemy.
Then, Donahue's ninja minions attack again and kill Teabag's butler, but Teabag helps the two boys escape by putting marshmallow Peeps in the microwave; which causes an explosion that destroys the mansion and kills both Teabag and the ninjas.