So...
I'm thinking of a You've Got Mail AU with Reese and Finch (and Bear, of course!). Obviously, they both have to be using some kind of online chat, perhaps even online dating, but without giving away who they are. Maybe they have become curious after protecting Maxine...

They are still working the numbers together and at some point one of them picks up on the other's identity.

I would love if it's not all lovey-dovey. Their work may become a problem, like Reese won't answer mails for a few days when he's out on a stake-out, or it's just that they have to make up things and don't keep track of what they said or something like that.

I think it would work with both of them as the one who finds out about the other's true identity:
a) Finch finds out and thinks that he can't actually have feelings for Reese and doesn't reply anymore at first, or
b) Reese finds out and thinks that he can't ever tell Finch because he wouldn't want him anyway...

That's basically it. I'm absolutely open for different ideas though :)