Sam realized that while he'd always been Sam, Sam wasn't all that he was when the light which had flared up from the pit when the final seal was broken all flowed into him. The light which was a Grace that he hadn't realized he'd left behind despite all of the clues that should have been freaking obvious in retrospect filled him nearly to bursting. As it continued to pour into him, he felt as if he would tear apart, but miraculously didn't do so.
He decided to hide everything from Dean after he looked at Dean and realized who his brother was. Knowing how stubborn Dean could be in any reality, it had probably been the only way. It had been so long since his brother had shown him such love, such unconditional devotion, and the thought of its loss hurt. He didn't want that to go away and see the hatred in his brother's eyes that he'd seen when he'd been cast down into the pit ever again. If hiding what and who he was was what it took, he would hide until the stars burned out.
He found himself oddly less inclined to destroy the world than he had been before he became Sam. It was strange how less than three decades could change a decision that had been made over several millennia before, and ease eons of hatred. While he wasn't willing to bow to the flawed and murderous creatures that his father so loved, he could see something of why his father had adored them, and found himself less inclined to go after a bunch of poor schmucks who were just trying to get on with their lives. Humans were flawed, murderous, prideful and sinful, but they also showed such love and compassion that would make even angels weep. It had been with a human heart that he had clung to his brother these past few years, a human heart that would shatter into a million pieces if he were forced to let go.
The fact that Heaven was trying to use him and destroy him in the process also factored into his decision to hide himself away. Hell would freeze over and the demons would start handing out ice skates and lollipops before he allowed his brothers to use him and force his brother who had always been his brother to kill him.
Less than a second after his Grace entered his body, he tamped it down, and hid it away with everything that wasn't Sam. If anyone tried to mess with him, or do something to what and/or who he considered to be his when Dean wasn't around however, they would get one devil of a surprise. Literally.
"We should probably get out of here." he told Dean the instant the lightshow was over.
Several hours later, Sam found himself being tortured by an angel named Zachariah and wondering why a part of himself kept repeating "If Dean wasn't here, you'd be a smear on the wall you little prick." as he tried to breathe without lungs. Soon afterwards, he and Dean were rescued by a revived Castiel whom he'd found himself adding to a mental Do Not Kill list that he hadn't realized that he had.
Soon, they were elsewhere, and Castiel was looking at him with his head cocked to the side as if there was something he didn't understand and was trying to figure it out. Based on the positioning of his wings which were faded slightly for some reason, Castiel was apprehensive.
Wait a second, how the hell could he see Castiel's wings? The damn things had been invisible until the angel had decided to show their shadows to them in that barn which had been rather ineffectively warded up the wazoo when they had first met.
"There is something different about you." Castiel said to Sam after a minute of staring at him in silence.
On one level Sam wondered what it was about him that caught Castiel's attention, while on another, he figured that his little brother had seen something that the others hadn't because he had spent more time with him than any other angel in recent memory. Either way, he decided to put it out of his mind, Castiel hadn't denounced him as Lucifer, so he didn't know. He'd just noticed that something was slightly off, and that was it.
"Y-You didn't say yes right?" Dean asked nervously, looking as if he were trying to look through him, as if he were trying to see whether or not he could spot the devil lurking within him.
"Of course not." Sam replied. It was the entire truth on more than one level. There had been nothing to say yes to. Not since he'd wriggled out of the little hole Azazel had made in the seals that held him in the pit, leaving his Grace behind.
Sam briefly wondered how Dean would react when he discovered that there was nothing for him to say "Yes" to either, and wondered where the hell that thought came from.
Either way, Sam would be staying by his brother's side where he belonged, where he'd always belonged, and he would be helping him stop the Apocalypse. Heaven wouldn't be using him or Dean to serve their purposes, not if he could help it. His reasoning was selfish, but the end result would be one that the Dean he'd spent most of the last twenty someodd years with would approve of.
Besides, he was Lucifer, and there would have to be something seriously wrong with him if he didn't try to screw with Daddy's plan.