They go to East High in Wichita, Kansas for three weeks while Dad tracks a wendigo. Sam's thirteen, and he doesn't usually bother trying to make friends; what's the point? But this time, he sees a poster for a youth group that meets at lunchtimes. Why not? he thinks. It's not like he has any particular aversion to religion – it's just never occurred to him before – and hey, he's got more incentive to believe than most.
What surprises him is how much he ends up liking it. He loves the passages in the Bible; they make sense, in a deep part of his soul he's never tapped into before. It comforts him to know that God's watching over his Dad, and Dean, and there's a certain amount of reassurance in knowing he can pray for his family.
He decides to become a confirmed Catholic, but first he has to confess. He's nervous, and doesn't really know what to expect, but it's relatively painless. He confesses to lying – he doesn't go into detail, but he figures God will know – and sometimes not honouring his father. He walks away feeling at peace for the first time in years, and the next day he's confirmed in the Church of the Holy Savior.
John tells him not to come back, and he walks out with a duffel bag and an aching soul. It's four hours before the bus to Palo Alto, and he's trying to find a diner when he walks past the church. The door is open, and Sam walks inside before he can stop himself.
The confessional's open, and Sam has tears in his eyes as he relays the confrontation with his Dad. He knows he should honour his father, but John... well, he makes it pretty hard sometimes, and Sam just can't live his life anymore. He walks out of the church more certain than ever that he made the right decision.
He assumes the nightmares are about Mom, until he comes home to blood on his forehead and Jess' body burning on the ceiling. There's blood on his hands, too – maybe not literally, but he could have prevented this, could have saved her... but instead, he was with Dean.
Dean doesn't understand why, but he waits for his brother outside the church. Sam sits down in the little booth – and damn, those things aren't made for someone his height – and pours out his guilt. Maybe in the technical, legal sense he hasn't committed murder, but in his heart, he feels at fault. The priest is sympathetic, and readily absolves him.
For the first time, it doesn't help.
In Rhode Island, Sam's faith is shaken. Dean turns out to be right – a malevolent spirit, not God's will – and for the first time, Sam wonders if his conviction is misguided. He steps into Father Reynolds' confessional, and he begs forgiveness.
The Father's soft chuckle surprises him. "Son, faith is easy during easy times. It's when, logically, there's no reason to have faith – but you believe nonetheless... that's the real test."
Sam feels a lot better as he leaves the church, and the case, behind.
He's not sure why he's here, but he heads towards the confessional anyway. Maybe it's Dean returning from Hell, or maybe it's the proof that he's been right all along. But whatever the reason, he's here, and he pours his heart out to the unsuspecting priest.
He talks about his fear that he's becoming something... inhuman. He tells the Father that he's killed, and might be forced to again before the year is out. He confesses the lies. The deceit. Everything.
When he walks out of the church, he feels lighter, peaceful – much like he did the first time.