Author's Note: This is my theory on what happened in the cage and just what is going on with the supernatural creatures. This will probably be Gamble'd later in the season.
Sam knew what was happening the minute Castiel showed up with Chuck of all people. After the revelation that Chuck had been God the whole time and the required explanations of why the fuck didn't he do more to help them stop the Apocalypse and Chuck/God's explanation that the whole thing was about Free Will, blah, blah, blah, they got down to the conversation Sam had been dreading ever since he woke up in Stull cemetery.
"Sam, how did you get out of the cage," Castiel asked in his old monotone voice.
Dean frowned, "You mean, you guys didn't get him out?"
Both Castiel and Chuck shook their heads, "No, I planned on getting Sam out of the Cage, but Heaven was in such chaos, I needed to get that settled before anything else so I could be sure that none of the Host would try to get either Michael or Lucifer out as well," Chuck said with a sigh.
Sam bit his lip, he knew what he was about to do was stupid and pointless, but he was going to try anyway, "I don't remember much, I was in there one minute and the next, I'm waking up in Stull."
God scowled, "Don't lie to me, Samuel Winchester, I know you're lying. Where are my sons?"
"Wait a minute. You're God, why don't you know," Dean interrupted.
God sighed, "My rule doesn't extend to Hell and since Michael and Lucifer aren't on Earth or in Heaven, I have no way of tracking them."
Sam took a deep breath, not wanting to tell the truth, but knowing that they wouldn't leave him alone until he told them, "Michael and Lucifer are dead."
To say you could've heard a pin drop was a gross understatement. Dean, Castiel and God all stared at him in shock and horror.
"What?" God finally asked, his eyes wide with shock, "What did you say?"
Sam gulped, "Michael and Lucifer are dead. They destroyed each other." Now that the secret was out, everything else began to spill out.
"After we landed in the cage, Michael and Lucifer pulled themselves out of Adam and me. I think Adam's soul was already consumed by Michael, because he didn't get up. Michael and Lucifer weren't happy with me and so they attacked me at the same time." He shuddered as he thought of that ordeal. "I don't know how long it went on but then, they began to argue. They started yelling and then shoving and then they pulled their swords."
"Wait," Castiel said, "Lucifer does not have a sword. He was stripped of it when he was expelled from Heaven."
Sam shrugged, "He must've kept Gabriel's after he killed him or made a new one. Anyway, they began fighting and it just went on and on and then, Lucifer managed to knock Michael onto his back and went for the killing blow but Michael thrust his sword and," He trailed off, trying to block out the images of what happened next but he couldn't, "They impaled each other at the same time and then there was this flash of light and I woke up in the cemetery."
There was a long moment of silence while God, Dean and Castiel processed what was said. Finally, Chuck got to his feet with a sigh and placed a hand on Sam's shoulder, "Thank you for telling me, Sam. I'd hoped that being locked in the Cage would teach my sons a lesson, but I was wrong."
Sam looked surprised, "You're not angry?"
God frowned, "Why would I be angry with you, Sam? You did nothing wrong."
"But, Michael and Lucifer-" Sam started but God held up a hand.
"What Michael and Lucifer did to each other was not your fault. It was mine for thinking that my two most stubborn sons would change their thinking after all this time." He squeezed Sam's shoulder briefly before gesturing to Castiel.
After they left, Dean sat watching his brother, he could see that talking about what had happened to Michael and Lucifer was upsetting Sam. The soup people wouldn't have noticed, but Dean did. He knew all Sam's tells and he could see that Sam was trying to keep it together. He got up from his perch at the table and sat beside his brother and wrapped an arm around shoulders that weren't as muscled as he remembered.
Sam jerked as if trying to get away, but Dean just tightened his grip. "It's okay, Sammy. Let it go, I gotcha."
It started off slowly at first, then Sam began to shake, gently at first and then more violently. Finally, he laid his head on Dean's shoulder and sobbed. They sat there for a long time and just held each other until Sam slumped against his brother in exhaustion.
Sam slept for the rest of the day and the whole night, probably the best night sleep he'd had since before Lucifer escaped. The next morning, Dean was greeted with a Sam that acted more like the little brother he remembered, but he wasn't fooled; he knew that Sam was a long way from being okay, they hadn't even broached the subject of what Michael and Lucifer had actually done to him before they started fighting, but they were on their way.