Peter was never a particularly religious person. He had no reason to be.
When he was just a baby his parents — Mary and Richard Parker — were killed. Peter doesn't really remember either of them, the clearest memory he has of them is his mother kissing his temple while his father explained that Peter had to stay a bit with "Uncle Ben and Auntie May" and soon himself and "momma" would be back. They never came back.
(Peter doesn't even remember if he cried or not when he got the news. But he remembers weeks without sleep, he remembers hugging Aunt May and hearing her whisper over and over again — more to herself than to Peter — that everything was going to be okay, he remembers growing up too fast.)
Since then, he moved in with his uncle and aunt, but even that didn't last.
(Peter remembers crying. Peter remembers holding onto Aunt May and just crying as he listened to the doctor say, "the bullet that hit him punctured an artery and we didn't have enough time to do surgery, I'm sorry". Peter remembers crying for weeks every time he saw anything that reminded him of his uncle. And Peter remembers swearing to himself that he would never let himself love someone that way again. Because Peter loved his mother and father, and they were killed. Because Peter loved his uncle, and he was killed. Peter was cursed, it was better if he didn't latch on to anyone beyond his Aunt May — even then, he just accepted it because she wouldn't let him leave and if he were a little braver, he would run away. He swore to himself he would never have another parent figure beyond Aunt May ever again, he would never love unconditionally ever again.)
So yes, Peter was never a particularly religious person.
But this didn't matter now as he cried out and pleaded with whatever higher being was listening.
Because Peter broke his promise. He found someone else to love unconditionally.
He found Tony Stark.
Tony Stark who isn't perfect and doesn't pretend he is.
Tony Stark who makes mistakes, recognizes them, and learns from them.
Tony Stark who — like Peter — loved too much and had his heart broken.
Tony Stark who was hated and despised by many and yet still fights to defend everyone.
Tony Stark who is dying.
(Peter remembers that when he was a little child and saw Mr. Stark on television, Peter thought he was like the sun because his smile could light up the room; when Peter first met him, he compared Mr. Stark to the moon because his mentor had a dark side that almost nobody saw; a short time later, when Peter really got to know him and observed his mentor interact with Miss. Potts without the press taking photos, Peter thought that Mr. Stark was like a natural satellite — a celestial body that kept orbiting around another. Once Peter compared him to the stars.)
But there, at that moment, as he saw his mentor smile at him and say that everything was going to be okay, Peter realized that Mr. Stark was an entire galaxy.
And that galaxy was being taken away.
Because Mr. Stark was turning to dust.
(Peter wanted to believe he was wrong. He wanted to believe that he didn't see his mentor's feet disappear. Peter wanted to believe that he was sleeping, and this was all a nightmare, a terrible nightmare. He wanted to believe that it was not happening. — But it was. Because the world was not fair, and Peter knew it since he was a little kid. When the world gave you something — someone —, it waited until you were happy and then promptly took it — them — away. And it was not fair but that is how it worked.)
At least this time Peter could say goodbye. He could say "I'm sorry I wasn't good enough". He could say "I love you".
(He knew this image would be in his mind for the rest of his life. His mentor, his dad turning to dust. But right now was not the time to think about the future. It was the time to stay strong. It was not the time to wonder if Aunt May too would be turning dust. Right now was the time to do everything possible not to cry.)
So Peter just hugged his mentor as tight as he could without hurting him.
So Peter just buried his face in the crook of his father's neck and said, "I love you".
And he felt more than heard him reply, "I love you too, Pete. I'm sorry".
And then Mr. Stark was gone. And Peter's arms, hands, face, and body were covered with dust.
(In that moment Peter swore that he would bring his father back. Peter swore that he would get him back. And that was a promise that no matter how much time and energy it took, he would keep).