At the beginning of the episode, people are auditioning for the Passion Play, based on the life of Christ. Ned Flanders auditions for Jesus, but when he is turned down by the producer, after listening in, Homer decides to audition, and he gets the role of Jesus. Ned is startled at this result. Homer goes home and after his annoyance that he has a line in every scene, he learns his lines and the play is a success. After Ned apologises to God for being a 'doubting Thomas' the cross on which Homer is on breaks and falls on top of Ned. Then Ned is carted off to an ambulance, Edna steps in with him and the ambulance man tells him "close family only", Ned tells him that she is his wife, revealing that he and Edna are married.
At the hospital, half the town intrudes on Ned's room, and Edna tells everyone to clear out. Marge decides to throw a wedding party for them, something which Helen Lovejoy is extremely unhappy about. They soon realize that having an "open" marriage, as Ned calls it, is tricky, and they have to deal with the ups and downs. Meanwhile, after an argument with the head, Edna pulls Rod and Todd out of Christian private school and into Springfield Elementary.
Later, she takes some advice from Bart and tries to turn them into regular kids, to some success. Ned worries about Todd going to college, which is filled with things he hates. There is a sequence entitled Ned's Nightmare, where he dreams that his kids will major in comparative religions. At their wedding party, Ned gets very upset with Edna, due to comments by Rod and Todd, something which Helen Lovejoy captures on her phone. However, Homer and Marge orchestrate a charade in front of Ned, in which they have an argument over Bart and Lisa. Realising that all couples disagree over their children, Ned decides to forgive her.