When glee club co-captain Finn Hudson believes he has found the face of Jesus in a grilled cheese sandwich, he asks for three prayers to be granted: for the school football team to win a game, for his girlfriend Rachel to let him touch her breasts, and for him to be reinstated as quarterback. When his first prayer comes true, he asks the glee club to join him in honoring Jesus through song.
Club member Kurt Hummel is devastated when his father Burt suffers a heart attack. His best friend Mercedes sings Whitney Houston's "I Look to You" to him, hoping he will find strength in faith. However, Kurt reveals that he is an atheist. Cheerleading coach Sue Sylvester, also an atheist, takes umbrage at the glee club singing religious songs in a public school setting, and has Kurt make a formal complaint. When confronted by guidance counselor Emma Pillsbury, Sue admits that as a child, she prayed that God would cure her sister Jean, who has Down syndrome. Her prayers went unanswered, leading her to conclude that God simply does not exist.
Mercedes, Rachel and Quinn pray for Burt, with Rachel singing "Papa, Can You Hear Me?" from Yentl at his bedside. Kurt is resistant, and later at glee club rehearsal sings The Beatles' "I Want to Hold Your Hand", stating that his faith takes the form of love for his father. He accepts an invitation from Mercedes to attend her church, where the choir sing "Bridge over Troubled Water". At the church service, Mercedes asks the congregation to pray for the Hummels.
Finn's remaining prayers also come true. Rachel comes to Finn's house one evening, and in his bedroom she admits that she would prefer to raise her children in the Jewish faith; she would not be able to have a future with him if he puts his faith in Jesus. Finn agrees that their children would be raised as she chooses, so to confirm her trust and appreciation of him, she allows him to touch the side of her breast as they make-out. Later, Finn is also reinstated as quarterback, but it occurs because his replacement Sam Evans is injured during a game, dislocating his shoulder. Finn feels responsible and confesses his guilt to Emma, who tells him it is unlikely God is communicating specifically with him through a grilled cheese sandwich. A despondent Finn doubts his new-found faith, singing R.E.M.'s "Losing My Religion".
At Burt's bedside, Kurt tells his still unconscious father that he feels he should have accepted his friends' prayers. As Kurt cries, Burt begins to regain consciousness and is able to squeeze his son's hand. Meanwhile, Sue visits Jean in her residential home and discusses God with her sister. Jean asks Sue if she may pray for her, and Sue accepts. Later, the glee club comes together to sing Joan Osborne's "One of Us". Sue watches the performance, but tells Will she will not report him for allowing a religious song. At home, Finn eats the remainder of the grilled cheese sandwich.
