When he smells Freddie Lounds on Will Graham, Mads’ performance is so struck in that moment because Hannibal was convinced. Will’s plan succeeded; he absolutely seduced Hannibal Lecter. That’s part of it for Hannibal. “You tricked me, and I allowed myself to be tricked.” The other part was just the devastating loss of the friendship.
I: We also see the return of Abigail, who’s fallen under the control of Hannibal just like the hold her father had over her.
HD: And also for Will. One of the cruelest things that Hannibal’s done to Will is this removal of a person who’s become a surrogate daughter to him—and, in turn, removed a surrogate father to Abigail. It’s not answered overtly in the episode since there wasn’t room for it, but the idea was that he’s done something different to Abigail that he’s done to Miriam Lass. He hasn’t kept her locked in a basement and reprogrammed her, he’s just convinced her that he’ll do what’s best for her somehow. To put it bluntly, she’s fully conscious and terrified of what’s happening at the end of that episode.