It is Easter time at the Marsh home; the family is decorating eggs and Stan wants to know why. He wants to understand the gap between Christ's death and the Easter Bunny delivering colored eggs. At the mall, Cartman makes his demands of the Easter Bunny; while Stan just asks him questions, hoping to get some answers. The Easter Bunny tells him that he is just a guy in a suit and that Stan should just go with it. Stan tells him that he is determined to get to the bottom of this. After Stan leaves, the Easter Bunny uses his break to make a phone call to a higher authority telling them that someone has started asking questions. As Stan is returning home, he is stalked by men in bunny suits. He makes it home and hopes for his father's protection, but he discovers that his father is known to the bunnies. In fact he is one of them and he tells his son about the secret society that he belongs to that follow the way of the rabbit, protects the secret of the Easter Bunny and they're known as "The Hare Club for Men." Randy takes Stan to a society meeting, where he hopes to his son will join their ranks. His father and many generations of Marshes before them have all belonged to the society. At the lodge, Stan is brought into a room filled with men in bunny suits. The "Grand Hare" openings the ceremony by having the rabbit, Snowball brought in. Stan is told once he hears the secret he will be bound to the club forever. The ceremony is interrupted by a ninja attack. As he must be protected Randy turns Snowball over to Stan's care. Stan and Snowball make it outside and Stan witnesses the members of the Hare Club being dealt with by the man who's controlling the ninjas.
Kyle is finger-painting when Stan arrives with a plea for help, then tells him what's been going on. Stan wants some answers but Kyle reminds him he's Jewish and has no idea. Randy and several surviving members of the "Hare Club" awaken to find themselves being kept in a cage in an unknown location. We can only assume Kyle used his Internet skills to get him and Stan to the home of Professor Teabag, where they hope he can tell them history of Easter. The professor thinks it is little late for lectures, until Stan mentions "The Hare Club for Men." Teabag shows them a copy of "Hare Club" member Leonardo Da Vinci's painting "The Last Supper" and reveals to them the secrets it contains. There is an egg in the painting that lies in front of St. Peter, who was the disciple that Jesus made the first Pope. St. Peter it turns out wasn't a man at all, but was actually a rabbit as revealed by laser technology. Clues are everywhere; the Pope's hat doesn't make sense, until you realize it was designed to cover rabbit ears. Jesus put a rabbit in charge because they are pure, whereas men are intolerant. The Catholic Church chose instead to put a man in charge and the "Hare Club" was formed to keep the secret alive. Kyle deduces that the Vatican took Stan's dad and that is exactly where Randy and the other can be found. The Pope wants to know where the rabbit is. Randy is going to be tortured to tell them where Snowball can be found, thanks to help from Bill Donohue and the American Catholic League. Stan doesn't get it, why would the Pope hold his dad hostage. Teabag speculates that Snowball might be a direct descendant of St. Peter. The ninjas attack Teabag's home. Stan, Kyle and Snowball escape. Teabag uses Peeps in the microwave to help the boys escape. Stan knows to help his dad he must bring Snowball to the Vatican, but first he takes some time out to ask Jesus for help.
At the Vatican, it is time for the Easter vigil and the Pope is feeding the poor with a massive rabbit stew, courtesy of members of the "Hare Club". The Pope finds it bit extreme, but Bill Donohue assures him its necessary to show the boy with the rabbit they mean business. Stan and Kyle arrive at the Vatican and Stan makes demands that are agreed to; but are immediately taken back afterward by Bill Donohue (courtesy of a double-cross) when the rabbit is in their possession. Suddenly Jesus appears, "He Has Risen", and he is disgusted with the state of his church and he reiterates why he originally put a rabbit in charge. Bill Donohue wants Jesus dead, since he goes against the church. Bill Donohue has everyone taken prisoner, including the Pope and he takes charge. The Pope and the two Jews, Jesus and Kyle, are placed in a cell, while the members of "Hare Club" are taken to witness the demise of Snowball. Pope Bill Donohue has taken over and is preparing to kill Snowball and the "Hare Club". In their cell Jesus tells Kyle he can only use his powers after he's been killed and he asks Kyle to do just that. Kyle reluctantly complies, but doesn't want Cartman to ever find out about it. Snowball is about to boiled, when Jesus resurrects in Vatican Square. Jesus removes Bill Donohue from his position as Pope and Snowball is installed into his proper position as Pope, where he makes no decisions on how men should run their lives, just as Jesus intended it. Stan has learned that he should just color eggs and stop asking questions.