Here is the epilogue...The ending is a bit ambiguous, don't kill me :) There is a possibility I might do a sequel, we'll see...

"Well, it was sure good to see Phil again. I'm glad he seems to be doing well." Pepper said, sitting down across from Tony on the jet.

"Yeah, it was." Tony said, but truly he had other things on his mind.

"Hey Pep, I have a question for you."

"What is it?"

"Did you notice that something is different about Coulson? I mean, of course he's different, for G-ds sake he actually died. But did you notice that he…he just felt different? Something about him just didn't feel right."

"I…Yes, I did, did notice that," She admitted. "I thought it might just have been that new heart of his, but I think it's something else." Tony nodded, his suspicions confirmed.

"I wonder what the hell SHIELD did to him."

They sat for a while in silence, pondering the frightening matter.

Finally, Pepper spoke up.

"I don't think we should think about this right now, Tony. What's important is that Phil is happy, we are happy, and that SHIELD, whatever they did to him, would not want to hurt him."

Tony nodded, and Pepper started to get up.

"I'm going to go get something from the kitchen, you want anything?"

Tony shook his head, still in thought.

"Don't worry too much, okay Tony?" she said, and gave him a kiss.

The minute Pepper was out of the room, Tony pulled out his StarkPhone™.

"Jarvis, are you done with that scan I asked you to run on Coulson?"

"Yes, sir." The AI's infallible voice answered.

"Show me the results."

"I'm afraid I cannot do that, sir."

"And why is that?"

"The results have been erased, sir"

"Erased?" Tony said, confused. "By who?"

"An external protocol. Apparently they contain classified information that you are not allowed to access."

Tony was taken by surprise. He was sure his firewall was absolutely unreachable. Evidently, whatever was going on with Coulson was top, top secret. So secret SHIELD was expending a great amount of effort to make sure absolutely no one could find it out.

"This can't be good," Tony mumbled to himself.

And although he didn't know it, Tony Stark could not have been more right.