So this is kind of a missing scene/ alternate scene to the one where Sam and Dean are in the church and Sam's telling Dean he saw an angel not a spirit. The first few sentences are the same as the show though.
"It spoke to me, it knew who I was."
"It was just a spirit, Sam. Okay, it's not the first one that's been able to read people's minds. Okay, let me guess. You were personally chosen to smite some sinner. You just got'ta wait for some divine bad signal, is that it?"
"Yeah, actually," says Sam.
"Great," Dean replies. "I don't suppose you asked what this alleged bad guy did."
"Actually I did, Dean. And the angel told me. And he hasn't done anything. Yet."
"Oh this is – I don't believe this," says Dean.
"Dean, the angel hasn't been wrong yet!" says Sam loudly. "Someone's going to do something awful, and I can stop it!"
"You know you're supposed to be bad, too, Sam, maybe I should just stop you right now," says Dean.
"You know what Dean, I don't understand!" says Sam. "Why can't you even consider the possibility?"
"What, that this is an angel?" Dean says.
"Yes! Maybe we're hunting an angel here, and we should stop! Maybe this is God's will."
This is where my alternate/missing scene begins
"Give me a break Sammy, God's will?" Dean retorts cursing his eyebrows upward and giving Sam the ultimate "that's a load of crap" look.
"Why can't it be Dean, I mean hell, look at all the bad things we see, why can't there be any good?"
"I never said there wasn't any good Sam; I jus' said there's no God or greater power."
"Why the hell not Dean! Why do you always have to be so damn cynical!"
"It's not being cynical, it's being realistic."
"Dean I don't get you man, you'd think after everything we've been through, you'd want to believe in something greater, something that could help us."
Dean just looked at his brother. It's because of what we've been through I don't believe in God Dean heard himself say in his head.
"Sammy you ask me why I DON'T believe in God, when the real question should be why the hell DO you!"
"Dean there just has to be a greater good out there, a greater power that can fight alongside us in this battle we're in with the dark side."
"Sammy, nothing can help us besides us, it's how it's always been and it's how it'll always be, end of story!"
"That is not true my son."
Sam and Dean both turned to see Father Reynolds approaching them.
"Great," thought Dean to himself, "just what I need, tag team action."
"Dean, God loves you and he's always watching out for you"
Dean had to try with everything he had not to let out a sarcastic laugh. If there was a God, he surely didn't love him, after everything God let happen, there was no way he loved Dean.
"With all do respect Father, you and Sammy, you can keep on believing in God's grace and goodness, I mean hell if it makes life more bearable and easier, then believe all you want, just don't expect me to believe."
"Why not Dean?" Sam asked gazing intently at his brother.
"Sammy just drop it okay, I don't believe in God and that's that."
"If you don't believe in God, Dean, why did you want to join the parish?"
Knowing that he couldn't answer that question truthfully he replied with the next best thing that came to his mind.
"Apparently my brother here believes enough for the both of us." Dean replied rolling his eyes at Sam. "I don't see why though, since there's clearly no such thing as a God."
"Dean you mustn't say that…he's as real as you and me." replied Father Reynolds.
"Oh yeah, if he's as real as you and me, why doesn't anyone ever see him in person?"
"Son, it does not work like that. God doesn't take on human form, but it doesn't mean that he isn't around…he appears to you when you need him"
That did it; those words right there did it. Dean wanted so badly to hold in his feelings on this, to not let Father Reynolds, but mostly Sammy, know why he was so adamant about God not existing. But before he could stop himself the words rushed out.
"What about when my mom needed him! Where the hell was he when my mom was burning to death! Where was he when my dad gave up his life for me!" Dean yelled back, not intending to raise his voice, but it happened none the less. The questions Dean yelled out were meant more as statements than questions and Dean couldn't hide the hurt in his voice.
Sam starred shockingly at his brother, seeing the pain in Dean's eyes and hearing the tremor in his voice made Sam swallow in the big lump that had formed in his throat.
Father Reynolds was quiet for a moment, taking in what Dean has just said to him, but he soon had a response for Dean.
"Dean, I am so sorry about your parents, but son, God has his reasons for not intervening."
"Reasons…are you kidding me!" Dean snapped back. "What possible reason could there be to stand back and watch as a 4 year old and 6 month have their mother ripped out of their life. What possible reason could there be to watching a family being ripped a part, filling their lives with a constant emptiness!"
Dean could almost hear Sam gasp, and he knew Sam's eyes were fixed on him. Dean knew though that if he even stole a glance at Sammy, the tears he was hiding behind his green eyes would come streaming down his face, and he wasn't about to show any more weakness and fragility than was already being witnessed by his baby brother.
As he watched Dean, Sam's tear filled eyes were about to prove to get the better of him. Seeing his brother so torn up broke Sam's heart. He immediately wished that he hadn't pushed this on Dean , hadn't tried to push Dean into believing in something that was clearly painful for Dean to even think about.
"Dean , what about all the good things God has given you?"
"Good things? There haven't been any good things, Father"
"You have your brother don't you?" asked Father Reynolds smiling at Dean.
"That wasn't God! My parents gave him to me, not God."
"And who do you think gave you your parents?"
"THEIR PARENTS!" Dean yelled out. Dean was getting sick of this "who gave who" game. "I'm not doing this Father, Sammy lets go". Sam immediately rose at his brother's command, wiping the tears off his face as he stood to follow his brother. Dean turned his back to Father Reynolds and began walking away.
"Dean, maybe God needed them"
Dean's heads immediately snapped back towards Father Reynolds.
"Maybe he needed them Dean, to fight with him…to be his angels"
"Don't," Dean began, but Father Reynolds didn't falter.
"Dean he needed…"
"I NEEDED THEM!"
Sam froze on the spot as the words left Dean's mouth. His stomach knotted and if it was possible to feel your own heart break, Sam was sure he was experiencing it. Dean was so torn a part, so…hurt. He watched Dean as he struggled for words to come out.
"We needed them, Father, me and Sammy, our family was torn apart, and now…me and him…that's all we have left…that's all I have left." Dean's voice was more solemn now and quiet. He then turned towards Sam, fully intending on Father Reynolds, not just Sam, to hear what he had to say next.
"You ask me why I don't believe in God, Sammy, how I could possibly not believe in a greater good…it's because it's easier to not believe in a God than to believe in one who would stand by and watch as my world shattered around me…as our world shattered around us."
Dean then turned to face Father Reynolds.
"With all do respect Father, I think you would prefer me not to believe in God, because if you convinced me that he does exist, I'd havet'a say that he's the cruelest form of good that I've ever come across. Having the power to help and not helping, I don't see how that's right."
Father Reynolds was about to interject when, to Dean's surprise, Sam stopped him.
"Father, I think my brother and I should get going now. It's been a long day and we're both really tired."
Sam didn't want this conversation to continue, he didn't want to see the pain his brother was in, he didn't want Dean to have to explain himself anymore to Father Reynolds, he just wanted Dean to be okay.
"Of course Sam," Father Reynolds replied with a sad smile. "Dean I'm really sorry you feel this way about God, maybe one day you'll see otherwise."
"I wouldn't count on it Father," Dean replied with a similar sad smile laced across his face.
As Sam and Dean walked out of the church doors and towards the impala Dean, from the corner of his eyes, could see Sam fiddling with his fingers and glancing at Dean every two seconds. Call it brotherly instinct or just excellent observation skills; Dean knew that Sammy wanted to say something.
"What is it Sammy?"
"Huh," Sam asked innocently.
"Dude you've been fiddling with your fingers and looking at me every second, so what is it?"
Sam was sometimes annoyed but always comforted at how well his brother knew his every little motion.
"I...uh…"Sam was having a hard time getting the words out, he knew what he wanted to say but it just wasn't coming out. He thought maybe he'd start with something simple. "I'm sorry Dean."
"For trying to make you believe in God when you have a completely understandable reason for not believing in Him."
"Maybe you're right Dean, maybe he doesn't exist, everything you said just…well it just made sense."
"Sammy, look man, don't not believe in God just cuz' I don't. I'm glad you have something to believe in Sammy, something you think is pure and good."
"Yeah I'm glad I do too…" Sam looked over at Dean and smiled. "But that something isn't God, Dean…that something is you"
Dean looked up to meet his brother's admiring eyes.
"What?" was all Dean could reply with.
"Dean, I don't know for sure if there's a God out there, I mean I like to believe there is, and maybe there is , maybe there isn't, I may not ever really know for sure so I may never really completely believe in Him, but there is one thing I know for certain…I believe in you Dean. I believe that you'll always do whatever is necessary to keep me safe and happy, I believe that you'll always put my needs above yours, and I believe that with your help, I can rewrite my destiny of turning evil. I believe in you and everything about you Dean, plain and simple, together I know that we'll beat anything that's thrown our way."
As Sam placed a firm hand on Dean's shoulder, Dean looked over at him with a smile so sincere that it melted Sam's heart. No more words were necessary in that perfect moment, but Sam had one more thing to tell Dean.
"When I told you I really wan'na believe in God because I want to believe that there's a greater good fighting along side us, that wasn't the whole reason…in fact that was only a really small part of the reason…there's a much bigger reason…the main reason actually"
"What's that Sammy?"
"…well…you protect me Dean, you always have, and I know you always will…but who protects you? I try my hardest, I do, but sometimes it's just not good enough, and when my efforts aren't good enough…I…I need to believe that someone higher than all the good and evil in this world, will protect you…will watch out for you, because I can't imagine this world without you Dean, I can't imagine going through life without my big brother by my side, and…maybe…if I believe hard enough…he'll always answer my prayers and watch out for you because he'll see how much I need you and…how much I love you."
There it was…the three words the Winchester men rarely ever spoke of, let alone actually recited. Dean felt the hot tears behind his green eyes as those words left Sammy's lips. He would never admit it but hearing Sam say that, hearing Sam tell him he loved him, made everything okay, made all of it bearable. Dean knew right then and there that as long as he had Sam, he would be okay.
When Dean didn't say anything back, Sam decided to cut the silence.
"Sorry, I know how much you hate chick-flick moments," Sam chuckled. "I just wanted you to know to truth."
Sam smiled at his brother then peered out the window of the moving Impala. And that's when he heard it, something he hadn't expected to hear, and something he knew was true but had gotten accustomed to not hearing.
"I love you too Sammy" Dean said as he looked at his younger brother and smiled. Sam smiled back allowing one tear to fall down his cheek.
All was right in that moment, Sam had Dean, and Dean had Sam. God or no God, they were going to make it, one way or another, they were going to prevail…against all the evil in the world, they were going to prevail…together.