The short answer is because he couldn’t bear the thought of Will living on without him, not thinking about him, not looking for him, not finding him.
Not caring about what happened to him.
He spent the whole first six episodes learning that his life was hollow without Will in it. If he ate Will, Will would be a part of him forever, much like Mischa was. But now that he’d promised to save Will–someone saved Will Graham, can you believe it? And it was Hannibal, who we’ve been telling to SIT DOWN this whole time!–and he did it, the option of eating Will was taken off the table. That could not be his resolution. Hannibal doesn’t want a resolution any other way; he wants the two of them to be in each other’s orbit for the rest of their lives. He’s no less obsessed with Will now than he ever was, and he can’t bear to let Will go. He will cage himself, to make Will his keeper.
As for Will, he has been through literal torture for this entire season–enduring Abigail’s death firsthand, getting gutted, alienated from everyone (including Hannibal), getting almost killed over and over–and by most people, slowly–and being the person that Hannibal wanted him to be (and that he never wanted to be). He wanted to know Hannibal before he saw him next, he wanted to see him with clear eyes–and now he has.
For Will, the difference between the past and the future was before
Hannibal and after Hannibal. For Hannibal, there is no difference–it’s a blur. Will has seen Hannibal reaching back in time, wanting to reverse everything and so playing out these dark and painful moments in his life into perpetuity. But Will has that full understanding. He doesn’t need to seek it anymore. Hannibal hoped to catch Will up in it again, in real life or in his mind–in some way, he must be a part of Will’s life. But Will doesn’t want to live like that, trying to make the teacup come back together. He’d finally reached the point where he just wants it to stop.
And he missed his dogs.
I can’t say enough how important that line was, and the shot of their empty beds in his little house. Will’s dogs were always “the best part of Will” as Alana put it in season two–they were presented to us as the lightest part of him, the best and most pure and good.
Hannibal took it on himself to corrupt the dogs in both seasons, feeding them people and then Mason Verger, just as he corrupted Will. He asked Will to leave them in “Mizumono,” and Will eventually did leave them to search for Hannibal.
There in Will’s house, when Hannibal was present, the dogs were not. Where Hannibal is, the best and purest parts of Will must leave.
In the end, after all the suffering and darkness and pain and fear, Will just wanted them back. He missed them.
He missed himself.