“You're the mongoose I want under the house when the snakes slither by.”

no the direct meaning in the context of their conversation is "I don’t think you’re fragile like Jack I think you’re stronger than anyone else believe, you can be a defender and not just the nerd weird guy who interpret dried blood on crime scenes"

result —> Will shot down GJH with his own hands. Hannibal slightly opened up a crack in Will’s controlled personnality (persona) and life. Just a tiny little push. So little it’s impossible to source. That’s why Hannibal then almost obliviously harasses Will about how killing GJH made him feel, because he triggered the whole thing himself and nobody is even aware. He’s a fucking demon, a well cooked Lucifer in the flesh.

He said this literally seconds prior the mangoose quote : "the devils is in the details" "the mathematics of human behaviour, all those ugly variables". He was actually talking about himself, because he was the copycat and Will was in whole confusion about how the copycat gave him an almost "gift-wrapped crime scene"

What a beautiful fascinating tv series.

I’d be more weirded out by “bone arena of your skull” personally.

I could be wrong, but I think there is this description regarding Will Graham in the book too, but it was said by someone else, I think a former co-worker from New Orleans, I'm not sure

I don't think Will flinched at this comment for two possible reasons: he either did not fully understand what Hannibal meant when he said this phrase, or he interpreted it the wrong way. When you first think of a mongoose, assuming you already know what it generally is, you might picture a stoat, a ferret, or a weasel -- all similarly shaped rodent-like animals that are passive, cute, and seemingly harmless. So, upon first assumption, it seems like Hannibal's saying "Oh, you're the fragile little rodent I want safely hidden and tucked away when dangers go by".

BUT mongoose are actually carnivorous animals that are rather ferocious for their sizes, a bit like meerkats and civets. They are known for attacking large snakes like cobras and whatnot. So, the truth of this phrase, once you do some digging, is essentially that Hannibal is referring to Will as his inside-man, and the snakes are not the criminals Will deals with or Hannibal himself, but rather the FBI and Jack Crawford. Will is unknowingly "attacking" the snakes, since he's under Hannibal's influence and Hannibal -- being the Chesapeake Ripper and the Copy Cat -- can use him as an outlet that feeds him information on what he needs to do to avoid the FBI's suspicion. He also is planning on using Will as a scapegoat, if need be -- the mongoose being under the house can mean a couple of things: he's hidden and safely observing, involuntarily funneling Hannibal information... but it can be a place where the snakes turn, trap, and corner him. In other words, it sets Hannibal up for framing Will when the snakes notice the mongoose that's been cunningly lurking under the house this whole time.

As to why Will didn't mention any of this to Jack or Beverly -- I think he just never got a chance to, one thing led to another. The next chance he might've had to speak to Jack about anything, he'd been traumatized after killing GJ Hobbs, and then Hannibal started weaseling (no pun intended) his way into Will's brain. By the time Will started putting pieces together that Hannibal was the "bad guy", Hannibal had already framed Will and revealed to the snakes that the mongoose has been hiding under the house. So I suspect this line played a part in Will's mind somewhere when he figured Hannibal out (although it wasn't one of the most outstanding of things Hannibal said or did, since Hannibal had spent basically the entirety of season 1 dropping sly quips and hints about who he was), he just never voiced it aloud. The phrase just got lost in translation amidst all the chaos of Will being framed, Will barking about Hannibal whilst being framed, no one listening to Will, and so on and so forth.

Cute on the outside, evil bastard on the inside.

Ooo okay, here’s my take on that scene!! Will doesn’t flinch, but you do see him kind of go quiet and contemplative, and I think he seems sort of caught off guard and uncomfortable with the comment. I interpret this as Hannibal absolutely nailing him as being “above” common murderers, higher up on the food chain if you will, due to his ability to assume their pov. And I think Will actually knows this about himself, but he represses it because it makes him uncomfortable and feels like a dangerous thing for him to acknowledge about himself or have recognized by others. Given how different his behavior is in the following seasons, I think a lot of Will’s season 1 stance of vulnerability (that isn’t caused by the encephalitis of course) is probably a lifelong unconscious social tactic to remain in some degree of connection with others, to make himself seem vaguely weak and passive so that others don’t see him as too much of a threat. So, I think when Hannibal not only notices his true capability / darkness but also COMPLIMENTS it after like ten seconds of knowing him, Will feels both seen and appreciated, and uncomfortably exposed. I think he doesn’t tell anyone else about this comment because it rings far too true to him, and would be far to revealing of his true nature, which he isn’t even comfortable with acknowledging himself. I think season 1 Will doesn’t want anyone to know (including himself) that he’s an “apex predator”, because that’s a very lonely thing to be.