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Some people see this between Neal and Peter. It remains to be seen which direction, if either, the writing team decides to put more emphasis on, but Peter dedicated years of his life to catching Neal, and Neal seems to know Peter at least as well as his own wife does.
There's a mock-up poster that was part of show creator Jeff Eastin's pitch to the USA Network. The tagline? His sentence ended with a proposition. Double entendre FTW!
And for someone who dedicated all his efforts to putting the guy behind bars, Peter seems to be putting just as much effort into protecting Neal...even from Neal's own girlfriend.
To more than a few fans, Neal and Peter's interactions read like nothing so much as a continually-evolving 24/7 BDSM relationship.
Hey, Peter says in the first episode that Neal belongs to him for the next four years.
In the 2nd summer finale, Peter says to Neal: "I can do whatever I want with you."
Peter's wife did tell Neal that "[Peter] is the best thing that ever happened to you," so I wonder which way she leans on this train of thought...
And besides Freud, we have Peter saying that Neal in danger makes his stomach hurt and his mouth go dry.
In "Unfinished Business," at the very start of the episode Neal thinks that Peter is taking him to an expensive, popular new restaurant. And throughout the whole damn series there's the looks, and the in-tune with each other's emotions thing, and the sacrificing for each other thing, and the abusing FBI resources for each other thing, and the commenting on each other's looks thing, and the talking about your partner while your eating lunch with your wife and her not minding at all thing, and the everything. You start to wonder when you have to drop the "sub" from "subtext."
"Company Man". Just, that entire episode practically moves beyond subtext. This troper was glad to see evidence that Neal cares about Peter as much as Peter cares about Neal.
Heck, in that episode there's a scene where a character describes how someone she cared about was poisoned, and how she wants revenge - then asks Neal what he would do "if someone took away the person you loved." Neal thinks about it for a moment - then looks up at Peter, standing behind her.
Some fans think Mozzie has a bit of a crush on Neal.
Some fanfiction makes Mozzie The Woobie when it compares him to Peter and how Neal will eventually not need him in his life anymore.
Alternately, Mozzie and Peter have teamed up in season two to look after Neal, with frequently hilarious results. Aw, Neal has two (bickering) daddies!
In "The Dentist Of Detroit," Neal and Peter are leaving the Burke home dressed in tuxes for their latest sting when Elizabeth stops them with a camera, saying, "Prom picture◊!" Make of that what you will...
In the same episode, the scene of Peter pretending to fire Neal was pretty much a break-up scene. It also teases the OT 3.
Neal: Look, I-I donít know who is stealing the money from the registers, but itís not meÖ
Peter: No, it is you. It is you! You know what?! You were trouble ever since you came to work for me with your glossy smile and those annoying little hats.
Neal: You LOVE my hats!
Peter: The hell I did! All right, youíre insubordinate, you never do what I tell you to do and every time I turn my back, youíre off doing who-knows-what with God-knows-who!
Neal: You know, you ungrateful bastard. I have had your back since day one and anytime anything goes wrong, Iím the first person you blame!
Peter: 'Cause youíre a con! Itís who you are and itís all youíll ever be. Youíre fired! Get out of my sight!
Neal: You know what? With pleasure. And the next time your hot wife gets lonely, tell her to call me.
In "Hard Sell," this line from Neal to Peter is just begging to be taken out of context.
Neal: You're trying to screw me.
In "Point Blank" Neal protests that Peter is pulling him off of a case and Peter responds with "I can do whatever I want with you." Oh my ...
In "Prisoner's Dilemma" Peter admits that if he ever had to go on the run, it would probably be because of Neal. Not much in itself, but in context? They were just talking about a Fed who went on the run after he fell in love with his CI (the position Neal has). Interesting...
Neal: What happened?
Peter: He had an inappropriate relationship with a C.I.
Neal: How inappropriate?
Peter: Do you want me to draw you a diagram?
Peter: He fell in love with her, he got caught, and then sent him down to bank fraud.
Neal: Then she was his first stop.
Peter: Maybe. She's his former C.I. They broke it off when she got transferred.
Neal: She has three known aliases. She knows how to hide someone. I mean, come on, Peter, if you went on the run-
Peter: I wouldn't go on the run.
Neal: Yeah, but if you did...
Peter: Yes, I'm sure it'd be your fault. Let's move.
In "Upper West Side Story", there's a quick line just before a scene change that makes Neal do a quick double-take. Neal has just conned his way into a suspect's house by impersonating a literature teacher and accepting a request for an at-home tutoring session made by the suspect's daughter. The suspect's daughter is clearly hot for fake-teacher.
Peter: I felt the same way about Mrs. Fitzgerald, my algebra teacher. Neal: Thus your life-long fascination with numbers. Peter: And smart, leggy brunettes.
The line definitely refers to El but, curiously, is an area into which Neal also falls...
Not to mention that El and Neal are very similar to each other; brunette, blue eyes, very intelligent, and very attractive. Peter seems to have a specific type, whether it be male or female.
There's a scene right in the pilot Peter gets a call in the early morning that Neal's outside his radius. He scrambles to finish getting ready for the day and rushes downstairs... only to see his wife and Neal Caffrey on his living room couch together with their heads bent down close looking at something. They both look up at him at the same time with almost identical expressions on their faces. The look on Peter's face says it all.
Neal and Peter's phone conversation in the season 4 premiere "Wanted" sounds an awful lot like a post break-up talk:
Neal: We had a good run.
Peter: Itís not over.
Neal: Yea it is. Youíre an FBI agent; Iím a con man. There are only a few ways this could have ended. This is one of the best.
Neal: You understand this has to be the last time. New York and I are done.
Peter: I get it. Please watch out for Collins.
Neal: I will. Itís good to hear your voice.
And from the same episode:
Peter: ďEllen, if anything were to happen to him, I donít think I could live with it.Ē