They're two years into a four year relationship before Peter begins to notice things. Things, he calls them, because he's not sure what else they would be. Suspicions. Flickers out of the corner of his eye. Weird feelings on the back of his neck. Things he can't vocalize but that make him sit up a little straighter whenever Neal Caffrey walks into a room.
He's picking up a paperclip from the floor when Neal approaches, and for a second he sees something, feathers and a shadow under patent leather shoes that implies that gravity isn't working as hard as it should be. He blinks and picks the paperclip up, and Neal is staring at him with an impish grin, and there's a feather in his hat but his feet are firmly on the ground.
There are people who Peter's eyes can't focus on, men and women who will sidle up to Neal and whisper in his ear while Neal stands still, more focused than Peter ever sees him on a case. They'll slip a piece of paper in his hand, which vanishes with a flicker, or they'll speak words that Peter's lip reading skills can't even begin to decipher. Neal will nod, vanish for half an hour (his tracker always places him at home, although he'll never answer his phone during these times), and then reappear looking calm.
There are dreams that leave him unsettled in the morning, visions of Neal standing in a crowd, wearing a different face but with the same shockingly blue eyes. It's only when he wakes that Peter realizes the crowd had been Greek, wearing togas.
There are the times where Peter comes in to the office late to follow up on a lead, and finds Neal standing at the glass windows of the FBI building, staring out at the city below. He's still at these times, unnaturally, and his eyes appear to be taking in more than Peter can see.
Peter sees all of these things and wonders, but they're like wisps of fog, too insubstantial for him to grasp.
And then one day Peter walks out the back door of the FBI building, looking for Neal who had claimed to be taking a smoke break (which Peter had assumed meant he was meeting Mozzie). But instead of Mozzie, there's a tall, older man standing next to Neal in the parking lot. He's wearing a suit that looks like it was made for him, gold cufflinks catching the sun like bursts of lightning.
Peter is too far away to hear them, but he can read their lips, and this time he understands what he sees. The older man puts a hand on Neal's shoulder, and Neal grins at him and says, "Of course, Father." The grin is impish, like a child planning a trick, but the man just nods, apparently satisfied.
"I'll see you soon," he says. He adds another word that Peter can't make out, but the wind shifts and carries it to him a split second later. Hermes, it says.
The sun brightens, comes out from behind a cloud, something, and blinds Peter for a moment. He shades his eyes, looking down at the ground. When he looks back up, Neal's alone in the parking lot, staring up at the sky with a longing expression. He looks down a moment later, catches Peter's eye, and grins that same impish grin.
Then he tips his hat, tucks his hands in his pockets, and walks off. Peter can swear there's a shadow of feathers at his feet.