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1* During a recent re-watch of this movie, I realized that everyone still refers to Lecter as "Doctor". This is a minor point, but wouldn't he have been stripped of any such titles once the news got out that he'd been, you know, eating people? I can understand Starling and Crawford referring to him as such, but Chilton even introduces him to Senator Martin as "Doctor Hannibal Lecter". You just ''know'' that he'd be the first one to stop using the title if it weren't necessary. So what gives?
2** I see it as a subtle commentary on Lecter's character. He has done things so heinous and ruthless that just hearing about them would make you squirm, yet he is undeniably brilliant and the FBI still has a great deal of respect for him. It's also interesting given the character of Clarice, who is portrayed as sort of an interloper in an otherwise male-dominated law enforcement world; perhaps the connotation of "Doctor" also serves to juxtapose her disrespected FBI character against a well-respected cannibal. It's also a constant reminder of the duality of his role in society prior to his capture, and there is a sadistic subtext in the characters referring to the psychotic madman as "Doctor." So I'd say half of it is purely to serve the script and the other half is the characters acknowledging his intellect (especially since much of the movie revolves around them trying to get information and assistance from him).
3*** It's also a way of distancing themselves from him, to keep their conversations as impersonal and formal as possible. They'll call him "Lecter" when he's not present, but when he's actually in the room with them, "Doctor" is a better option, giving away less about their feelings towards him than using his name might.
4** As long as there was nothing wrong with his thesis, I don't think they can.
5*** Even if his licence to practise psychiatry has been revoked, he's still entitled to the honorific.
6** Chilton introduced him as "Doctor Hannibal Lecter" because he wanted the introduction to be more dramatic. Same goes for the little flourish of his hand. In the novel this is when Senator Martin begins to realize that siding with Chilton was a mistake.
7*** In the novel, Dr. Lecter still writes articles for medical journals while incarcerated.
8** Because they are interviewing him and need to show him respect so that he'll co-operate; they may or may not be feigning, but as long as they need his help they are going to as polite and civil with him as possible in order to get it. It's the same with a great deal of what Clarice says to him- unfailingly, almost overly polite, and whether or not it's genuine is besides the point because she's trying to massage his ego either way.
9** Revoking someone's [=PhD=] is not an easy thing to do and requires making something extremely wrong with the research necessary to get it, or afterwards. Two cases that come to mind from recent times - Jan Henrik Schon and Diederik Stapel - in both cases they were stripped of their [=PhDs=] because they faked their research results and publications. If Lecter's research was all genuine, it would be difficult to revoke the title and would require a lot of red tape and prolonged court battles to do so.
10** Keep in mind that "doctor" can mean medical "doctor" (which Lecter was, and which certainly would have been stripped) and [=PhD=] "doctor" which is about educational achievement and can't be stripped without proof of fraud. The two types of "doctor" aren't even really related.
11* HOW did Lecter get that pen??? In the film, at least, it seems like the only way he could possibly have grabbed it would be if he used [[Franchise/StarWars the Force]]. Which, ya know, is totally legit.
12** Chilton was careless one day and left it in his cell. This is thoroughly explained in the novel.
13** While there's a quick cut from Lecter in his cell to arriving at the Tennessee airport, it's a fair assumption that some time passed between the two scenes. Lecter simply grabbed the pen when no one was looking.
14* During that RedHerring scene where Crawford and his men break down the wrong house looking for Buffalo Bill, why did Crawford look shocked when he mentioned Clarice's name? Did he somehow sense that she found the real home and is in danger or something?
15** Since Starling is Crawford's prodigy, as well as much more directly involved in the case than he was, he probably figured that she knew where she was. In addition, a previous scene has Starling mention how she knows Buffalo Bill's location, with Crawford retorting he already does. Since Starling was absent when he arrived, he then knew Starling had found the actual location and was already there.
16** It was very much an OhCrap moment for Crawford. The whole thing was a colossal screwup on the FBI's part, and going to the wrong house was just the last nail in the coffin, so to speak.
17* Possibly the result of an AdaptationExplanationExtrication, but how did Lecter manage to remain a free man with a squeaky clean reputation, and a licensed psychiatrist, long enough to later murder the flautist (Raspaill, in the novels) and be "found out" by Will Graham if he had already crippled and disfigured Mason Verger during a therapy session?
18** IIRC, Verger disfigured ''himself'', due to post-hypnotic suggestion from Lecter. According to Website/TheOtherWiki, Lecter treated Verger after the latter's arrest for various crimes, and was himself arrested "soon after" the disfiguring and broken neck. It's likely no one took Verger all that seriously, given his own sick criminal nature, despite his family's money and influence.
19** Also, wasn't it mentioned in one of the books that the only surviving victim of Lector was in a coma? If that's the case, maybe Verger was put into a coma by Lector after an attempt to kill him post-facial mutilation didn't succeed, and he ended up waking up years later after the events of Silence of The Lambs, being wheelchair bound as he is in Hannibal.
20* After overpowering his two guards in Tennessee, Lecter has time to disembowel one and hang him from the top of the cage, then swap clothes with the other, cut his face off, call up the elevator, put the corpse on the roof and arrange it face down with a gun at his hand, climb out, send the elevator back down, put the dead guard's face over his own, lie down and fire some shots in the air. Surely the guards would have been missed in the hours it would have taken him to do all this.
21** This is addressed in the DVD commentary that Johnathan Demme acknowledged that the scene in the prison cell room was an AcceptableBreakFromReality since he wanted something shocking.
22** Seems like someone as practised (although not recently)as Lecter could have done that in less than 30 minutes.
23* It’s never explained how Buffalo Bill transported Catherine, and presumably the other girls, to his home and then got them down into the pit. Catherine lives in Memphis which is about 500 miles to the nearest point in Ohio, and the real Belvedere is about 750 miles away. Therefore with his old van he’d have needed to stop for fuel at least twice and the trip would’ve taken at least 12 hours. While he could’ve brought food and just peed in bottles or something it’s doubtful he could’ve brought that much fuel with him. Given what we see of her it’s doubtful Catherine would be that quiet and passive if she knew they were stopped someplace public. It’s plausible that he could’ve restrained her thoroughly enough that she couldn’t yell for help and pound against the side of the van. But then she likely would’ve been in much worse physical shape than we see her in the pit. Then how does he get them into the pit? It’s also plausible that he’s strong enough to throw them down there or he coaxes them to climb down by pointing a gun at them or something.
24** Keeping Catherine restrained in the van wouldn't be an issue, as there are numerous real life examples of such a thing happening (such as the Tara Calico case). As for lowering her into the pit, the book says that Gumb used a hoist to lift his victims in and out.
25* Perhaps this is different in the book, but Hannibal Lecter's final hint, "We covet what we see every day" despite sounding pithy and profound, reveals that the FBI were apparently too dumb to check out the town that the first victim lived in. They state outright that they know she was the first victim, but apparently didn't think to ask if the killer might have known or seen her (every day).
26** Bimmel's father says that police had interviewed him several times. In the novel it's expanded further, as by the time Bimmel was found and identified it had already been well established that Buffalo Bill selected his victims at random. Furthermore, when Clarice asks to investigate in Belvedere Crawford initially shoots her down, because it had already been searched extensively. What led Clarice to her success was the profile from Lecter, which introduced a new theory to the investigation, and herself being the only woman investigating the murders of these women.

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