Everyone important in the show knew there was something going on between Hannibal and Will, even if no one knew exactly what it was.
We always joke about how it was so obvious they had a thing going on and no one noticed, but that's not true. Everybody noticed. It's in the details, but they definitely did. The thing that gives us the impression that they didn't, is the fact that no one actually does something about it.
For one Bedelia, who definitely got closest to the truth of their relationship. In s1 she already states Hannibal's feelings for Will are unconventional without ever having met him. She already knows it's obsession on his part, but back then she's still convinced Will is yet another victim of Hannibal's, just like she is. She warns Hannibal multiple times when she senses things are getting out of hand. She sees through him. In 1x12 she tells him ‘’Whatever you think you’re doing with Will Graham, stop. You’ve crossed professional lines.’’ and ‘’You have to maintain boundaries with Will, Hannibal.’’ That’s not about any of Hannibal’s framing plans or his murders, Bedelia doesn’t know about that yet. Hannibal hasn’t let her see him, she doesn’t know just how wicked he is. All she knows is that Hannibal is trying to protect Will (in the whole Abigail situation), and that Hannibal’s feelings for him are bordering on dangerous in the sense of risking his career and professionalism for Will. Bedelia strictly advises him against pursuing such a relationship, against getting too involved.
When Bedelia starts to see Hannibal’s true nature, her perspective on Will starts changing as well. In 2x02 when Bedelia goes to tell Hannibal she can’t see him anymore because she believes him to be dangerous, he tells Bedelia that Will asked for his help and Bedelia replies; ‘’Then maybe you deserve each other.’’ Bedelia was the first to know it was mutual from that point on. She goes to meet Will later that episode because she wants to confirm it. Will is catty to her, even when she says she believes him. ‘’I’ve heard so much about you, I feel I almost know you.’’ ‘’You don’t.’’ Will says, but Bedelia knows enough.
Bedelia returns in 2x12, interviewed by Jack. ‘’Nothing makes us more vulnerable than loneliness, agent Crawford.’’ Bedelia says. ‘’Will is not alone.’’ Jack says, implying himself. ‘’No, he isn’t.’’ Bedelia responds, and she implies Hannibal. Then she goes on tainting Jack about Will not being on his side anymore, and that the killer Jack should be wary of is not Hannibal, but Will.
Eventually in Florence, Bedelia learns that the focus of Hannibal’s ‘’obsession’’ with Will has shifted. When he likens Will to Mischa, Bedelia comes to understand that obsession has evolved and turned into love, which is even more dangerous for all of them. She consults with Hannibal about his love for Will and guides him into thinking he should ‘’eat’’ Will if he wants to forgive him. ‘’Betrayal and forgiveness are best seen as something akin to falling in love.’’
From that point on in S3B, during their ‘’therapy sessions’’, all Will and Bedelia do is bicker. ‘’We’ve both been his bride.’’ and ‘’I’m covered in scars, I wasn’t wearing armour.’’ ‘’No, you were naked. Have you been to see him?’’ ‘’Yes.’’ ‘’Haven’t learned your lesson, have you? Or did you just miss him that much?’’ They bicker bicker bicker about Hannibal and who he belongs to, but really, that’s one sided beef. Bedelia knows Hannibal isn’t hers. She admits it multiple times. ‘’If I’m to be Bluebeard's wife, I would have preferred to be the last.’’ Etc etc, in the end she’s the one who confirms Will’s question when he asks her if Hannibal is in love with him. I think that the funny thing is that Bedelia always knew Will was just as far gone, that’s why she was so stiff to him. Like having a beast like Hannibal falling in love with you can’t be helped, but loving it back, that’s what bothered her and made her despise Will so much.
Chiyoh knows about them the same way Bedelia does, because Will allows her to know. He wants her to. He shows Chiyoh his scar, confirms he and Hannibal ‘’Knew each other intimately’’ and were ‘’Very good friends [Nakama]’’ Like Bedelia, she too is on the other side of the veil. She knows what Hannibal is, knows what Will is, and she knows what kind of people they are to each other. Will comes looking for Hannibal in his childhood home and finds her. Of course she knows. He sits at her table and confesses ‘’I’ve never known myself as well as I know myself when I’m with Him.’’ If anything tells us she is one of the characters who sees through them best, it’s her telling Will ‘’There are means of influence other than violence.’’
Three other characters who always knew about them, less intimately and in more of a mocking manner, were Freddie, Gideon and Chilton. They continuously mock the erotic/romantic dynamic Hannibal and Will have. Freddie calls them out multiple times, with absolute cherry on top being the ‘’You called us Murder Husbands’’ ‘’You did run off to Europe together’’ discussion they have in 3x09. In the flashbacks in 3x01,
Gideon taunts Hannibal the same way: ‘’Snails aren’t the only beings who prefer eating in company. If only that company could be Will Graham…’’ And Chilton, who doesn’t comment on their relationship to them directly, but rather to Jack and other people he wants to convince Hannibal and Will are much closer than they think. In 3x04 Jack says: ‘’Maybe it’s one of those relationships that end after the disembowelment.’’ Chilton replies: ‘’I’d argue with these two. That’s a tenemous amount of flirtation. Will Graham is going to lead you right to him.’’ Later he says ‘’You dangle Will Graham and cut bait. You’re letting Hannibal have him hook line and sinker.’’ In that same episode he says ‘’You’re alive because you didn’t pull that glass from your neck. Will Graham is alive because Hannibal Lecter likes him that way.’’
Same goes for Mason and Margot. Margot is more discreet, but she’s the one caught up in Hannibal and Will’s drama at the height of it in s2b. She sleeps with Will while he’s thinking of Hannibal, her baby is taken away because it’s Will’s child and Hannibal doesn’t like that, she talks with him about Will’s ‘’Private carnage’’ with Hannibal. In the script there’s the famous ‘’I slept with one of your patients, Will Graham, how does that make you feel?’’ ‘’Curious, Will Graham is not a lesbian.’’ ‘’He sure made a go at it.’’ Besides the fact that they should have kept this because it’s fucking hilarious, it also implies Margot knows that Hannibal cares that she slept with Will, otherwise she wouldn’t have asked him how it makes him feel.
Mason is blatantly offensive with it. He makes sexual puns all the time, especially in 3x07. ‘’I snatched Will Graham right out of your mouth, you must be famished.’’ And, my favourite: ‘’You boys remind me of that German cannibal who advertised for a friend and then ate him, and his penis, before he died.’’ Mason is referring to a real life person here called Armin Meiwes, who met a man online and consensually ate him after they had sexual intercourse. It’s one of the most famous cases of gay sex crimes to date. It’s also funny because Meiwes was called the ‘’real life Hannibal Lecter’’ by the media for a long time. Either way, Mason keeps making jokes about an overcooked penis and eating Hannibal with Will’s face. (Hannibal finds all of this awfully amusing, by the way)
I think Alana and Jack have the most complicated thoughts about them, that’s why so many people believe they were oblivious enough to not notice what was happening. They weren’t. They knew, they just didn’t want it to be true. Why didn't Jack and Alana try to stop them? Why didn't they try to keep them apart? Truth is; it's because if you suspect something, but wish with all your heart it isn't true, you say nothing. You hope you've got it all wrong, so you don't say anything in case you do. They hope their suspicions are wrong, and if they're not, I think they knew certain things were inevitable.
It takes Jack a long time, even if he was always suspicious. In 1x12 he knows nothing, but he already says ‘’It’s not that I think Dr. Lecter is dangerous, I don’t. I’m worried about his relationship with a patient of his; Will Graham.’’ In s2b, Jack wants to believe Will is his man in the room. He has to believe it, he doesn’t know how things will end if he doesn't, but he’s worried. Suspicious. He assures Will multiple times that Will belongs to Jack’s side and that he ‘’knows what to do’’. He doubts Will enough to be insecure about the whole plan.
I think the moment Jack started sensing there truly was something going on between Hannibal and Will, something undeniable, was when he came to ask Will why he decided to call Hannibal. when Will says ‘’because I wanted to run away with him’’ Jack sighs and knows. He knows what’s going on and still hopes it isn’t true. He hopes it isn’t true in Florence, when he asks if Will’s going to slip away with him if he gets a chance and Will answers ‘’Part of me will always want to.’’ He hopes it isn’t true when he says ‘’You have to cut that part out.’’ Jack hopes it isn’t true until the very end. After three years of marriage and family he finally trusts Will enough to let him near Hannibal again, thinking he changed, but deep down, I think that Jack too knew that Will was a lost cause from the moment he decided to call Hannibal in Mizumono. He just never let himself believe it, and that was his mistake.
Alana, on the other hand, starts believing it more and more throughout the series. At first she’s incredibly confused as to what their relationship is, because she believes Hannibal is in love with her and she thinks Will might be as well. When she learns Hannibal and Will are conspiring behind her back, (‘’We know where we are with each other, shouldn’t that be enough?’’) she becomes paranoid. She goes to tell Will he should keep his distance from Hannibal, while Will on his part tells her to stay away. ‘’I don’t think Hannibal is good for you and I think your relationship is destructive.’’ ‘’Hannibal’s good enough for you.’’ The thing is that they both pretend to be protecting each other, while in reality they’re protecting their own relationships with Hannibal. In the end, when Alana realises she’s losing against Will, she starts to see things clearly. ‘’You're lying. You're all lying. Will. Hannibal. You're lying to each other and they're lying to you. This isn't in my head. You are hiding something and this will end badly for all of us.’’ She tells Jack in 2x11. However, at this point Alana suspects, but she doesn’t accept it yet. Like Jack, she doesn’t want to believe it.
That changes after Mizumono, when she starts working for Mason and gets together with Margot. In 3x04 Alana finds Will sitting in Hannibal’s kitchen in the place where Hannibal left him and Abigail in Mizumono. Will snarls at Alana ‘’What are you doing here?’’ as if she has no right to be there. It’s his place, his memory, his man. Alana is not supposed to interrupt that fantasy, like she wasn’t supposed to interrupt them in s2b. Instead of backfiring insults at him like she would have before, Alana sighs with defeat and says ‘’Friendship with Hannibal is blackmail elevated to the level of love.’’ Will huffs and looks away. He doesn’t agree with her, she doesn’t understand, because for him, it was love. It is love. But, in a way, Alana does understand, because she asks: ‘’After everything he’s done, can you still ignore the worst in him?’’ After that Will asks her to leave him alone.
In 3x07 Alana has another private conversation with Will after Mason takes both him and Hannibal captive. ‘’You helped Mason find us.’’ Will says. ‘’I helped him find Hannibal. We followed his wine when we should’ve just followed you.’’ She replies. ‘’I knew you couldn’t stop yourself, so I was trying to get to Hannibal before you.’’ And then something very interesting happens. Where, in s2a it was Alana who got angry at Will for attempted murder on Hannibal by proxy, Will gets angry and hurt at Alana for being an accessory to taking Hannibal captive. He doesn’t even care about what’s going to happen to himself. He just tells Alana: ‘’By facilitating torture and death?’’ Then Alana, confused by this switch of perspective from them both, says: ‘’I can abide the thought of Hannibal being tortured. I’d say he has it coming, wouldn’t you?’’ But Will keeps quiet. ‘’Maybe you wouldn’t.’’ She said. That’s where she realises something big has happened between them. Will, who once tried to kill Hannibal through another man, can’t even stand the thought of Hannibal being tortured now, while Alana can.
Even in the end, Alana is more uncertain than Jack about the escape plan. She doesn’t entirely believe Will’s family life healed him. I think she knew throughout the whole of season 3 that Hannibal and Will would end up together. She only allowed the plan to be set into motion because they didn’t have another choice.
So yeah, every character in this series is extremely clever, everyone knew, it was hard not to see. Could things have been prevented? No, I don’t think so. That’s why no one ‘’did anything’’. But the idea of a bunch of highly educated people who work in psych missing such a dynamic as Hannibal and Will's is very unlikely.
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