Will knew what had happened. He knew exactly how Abigail's ear had gotten into him, who had shoved it down his throat. He also knew that trying to indicate Hannibal as a killer again was futile. Jack seemed to want to believe him, going by the conversation in the BSHCI's visitor hall, but Jack needed something concrete, evidence. Hannibal had eluded capture for so long, he wasn't going to start leaving fingerprints or hairs at his crime scenes now.
No, Will was going to deal with Hannibal Lecter on his own terms. The man deserved to reap what he'd so carefully sowed, didn't he? He deserved to experience what he'd coaxed forth from the bottom of Will's soul, to see the result of his machinations.
After his release from the Baltimore State Hospital for the Criminally Insane, Will doesn't return to work for the FBI.
If you guys aren't reading Pattern Break then we can't be friends. It's a fantastic AU scenario of S2 where instead of working secretly with Jack, Will decides to entrap Hannibal on his own (of course this sort of fails and he ends up shacking up with Hannibal instead and becoming his lovely murder husband lol). Seriously, out of all the heatus fics out there at the mo, this one takes the cake. I'm always obsessively scanning AO3 for an update.