Dean is in Palo Alto after checking up on Sam when the Impala breaks down a few blocks from his apartment. He meets some of his brother's friends who tell him there's a sort of party going on (I think it was to celebrate his and Jess' engagement) . When they arrive at the apartment, Sam hears them talking about a guy whose Impala broke down and he kinda freaks out but when they arrive there, Dean is gone.
Non-wincest, has a couple of sequels. In the next one, Sam and Dean meet at a bar, have a pool game, and Sam convinces Dean to stay and have a rematch. The one after that one is an AU in which Sam makes Dean his best man at his wedding and the storry is as if John hadn't disappeared but had the brothers' adventures with Dean.

ETA: Found by hybrid_cookie!! :D