This scene is from the end of season 1 after Neal has been brought back to prison (another scene I wrote)

Peter walked around in Neal's empty apartment without an actual aim. He just wanted to understand, to make things make sense. Neal had been about to leave, and all he brought was one bag with nothing more than a passport, some cash and a minimal amount of clothes.

Was that the way he had been living before he got arrested? A life with no ties, always ready to leave. In Peter's world that was not a healthy life. A good life was a settled one. It did not seem as that was what Neal wanted. Or did he want it on his own terms? Had Peter pushed him into a situation where he felt he needed to escape?

Now Neal was in prison, and Kate was dead. Nothing had turned out as any of them hoped.

June stood in the open doorway.

"I thought I heard someone moving upstairs."

"I'm sorry." Peter forced to keep his face from reddening. "I just…" He did not find the words to describe what he was doing there.

"You're Neal's handler" June replied with a crisp edge. "You have the right to search his home."

"That's not why I came. I just wanted to understand what was going on in his head. June, Neal is back in prison."

June's stoic pose sank. She pulled out a chair and sat down.

"Oh, Neal. What did he do?"

"Nothing, as far as I know," Peter admitted, feeling guilty, being a part of the system that forced Neal back.

"Then you didn't put him there?"

"It was not my call." He sighed. "Neal was about to leave with Kate after a deal with a guy on OPR. It was all legal. Then the plane exploded on the ground, with Kate inside. Neal was there. And no one understands what happened."

"Neal would never kill Kate" June protested.

"No. He wouldn't."

"And you said it was legal for him to leave?"

"Yes. I did some research to check what he was doing. It was all legal." 'Was' Peter thought. He had seen it. Neal had had an official release from his sentence and had been a free man. Bought with a bribe consisting of a music box, but that was beside the point.

"Then why is he in prison? Because of the explosion?"

"That's one reason. The other is that his deal has vanished. For everyone else, it looks like Neal was about to escape. And that alone is a valid reason to put him back."

"Can you get him out again?"

"I don't know" Peter admitted. "I still haven't got my badge back. I probably will get it back, but…"

"You're not sure if you want Neal back out?"

"No, I do. I do. He is a valuable asset. And a friend. I just… I can't figure out if I'm doing him a favor or not. June, he left all this. For a dream. For a woman he didn't actually know. A woman that hide from him." Peter had never liked Kate. She had never made the impression to care for anyone but herself. "Before I arrested him the first time, he left for Europe without Kate. We kept eyes on Kate with the hope to catch Neal. When he got back, he didn't come near her. Do you know why? Because she was hiding from him. And not once have I heard him question why she did that. Because Neal sees what he wants to see."

"Or he sees the good in people" June pointed out. Peter nodded. Perhaps. Or Neal was just plain naïve when it came to women, and Kate in particular. "But why do you think Neal would do better in prison?" June persisted. Peter sighed, searching for words.

"I wonder how much my behavior caused him to feel he had to leave. When he has served his time, he is free. Free from me. Free to make his own choices. If he's in prison, I can't…" Peter did not want to see Neal in prison, but this was not about what he wanted but what would be best for Neal. And he wanted June to understand that. "He once expressively said he didn't want the life I offered. Maybe I made him feel trapped, instead of helped."

And a trapped Neal is a Neal that runs. And a Neal that escapes his sentence ends up in prison for good. That was the last thing Peter wanted.

He had been walking back and forth. Now he pulled out a chair and sat down, facing June.

"Since he started working for me, I've cuffed him twice without him being guilty of anything. He's a con-man. And to con a con-man so he becomes a prime suspect… He gets the blame for things he didn't do. And he gets the blame just because he works for the FBI, for me. We keep him under a Close watch which seems to make it twice as fun to frame him. He's Neal Caffrey, the greatest con-man ever lived. A challenge for the whole con-man-world out there. And I put him in a position where he cannot defend himself."

"But you proved him innocent the first time" June pointed out. "And I'm sure you can prove him innocent this time too. And that I think is most important; to prove he is innocent when he is. To fight for him. To show him that you're there for him, that you have faith in him."

Peter nodded. It would not be the last time Neal ended up as a suspect. And Neal could use the situation to commit his own crimes and claim he was framed. Peter could not trust him not to. How many times would he hurt Neal by not trusting him when Neal in return trusted him completely? But he did trust Neal, in a peculiar way. Not as unconditional as Neal probably trusted him, but he did trust him with his life and the work he was doing for the FBI. And he had faith in the kid.

"Your husband…" he began, looking at June. "Did he ever…stop?"

"And became an honest citizen?" June clarified the question. Peter nodded. "Yes, he did. For most the part at least."

"What made him quit?"

"Something you cannot control." June smiled. "Kids. A desire to be with them when they grew up and not meet them in an orange jumpsuit on the other side of a glass wall."

Through Peter's mind rushed images of single women he could introduce in Neal's life. He dismissed the idea at once. Neal had to figure things out himself, make his own choices. All Peter could do was to show him what life could be like, give him reasons to stay, and show that he had faith in Neal and would be there for him.