After seeing Fredricka Lounds get away with a lot in "Amuse-Bouche" and smugly telling Crawford he can't arrest her for writing the article about Will, it's great to see her get taken down a peg or two when he points out she's been contaminating crime scenes and he can indict her for obstructing justice.
In the pulled episode, "Œuf", the killer of the week is holding a child hostage and has Graham at gunpoint. Graham's just about to surrender to save the child, when boom! Beverly Katz shoots the woman in the shoulder from the shrubbery and takes her down in a second.
In "Fromage", Hannibal is confronted by Tobias, the serial killer friend of one of his patients. There is a fight and neither can gain any ground until Hannibal tricks Tobias into punching into a ladder. He uses the ladder to break his arm and cripple him, brings him to his knees with a throat punch and kills him by slamming a heavy statue — of a deer, no less — on his head. Since Hannibal has primarily been an intellectual threat rather than a physical one in all his appearances, it's good to be reminded that a highly intelligent and icily calm Serial Killer can still be pretty damn dangerous in a fight.
Also some Fridge Brilliance: some people thought Hannibal really should have done better in the fight (Tobias did seem to have an edge until the end), but watch carefully—after he took some impressive-looking damage (his arm, his leg, a few facial wounds) he proceeds to curb stomp Tobias: first using a rope-a-dope on a rather conveniently placed ladder (that he himself moved during the course of the fight) to pin and break Tobias' arm, then an almost nonchalant larynx strike that drops Tobias like a sack of potatoes. Following that, he not only uses a tablecloth to pick up the deer statue before smashing Tobias' head with it, he uses the tablecloth to tip over the table it was on—no fingerprints means it looks like Tobias fell against it, dropping the statue on his own head. He was making sure that he looked beat up when the law arrived. After all, an opera-loving psychiatrist shouldn't be able to easily dispatch a psychopathic murderer who took down two cops.
Will also does very well in the episode "Fromage", when he's garrotted from behind by Tobias, trapping his hand and his gun close to his head. So Will tilts the gun back and fires it, deafening them both and dazing his attacker, forcing Tobias to release him.
Gideon's escape from a transport van by breaking his thumb to escape his handcuffs, then killing both his guards.
Even cooler is when Will copies this method in the finale having analysed it the episode before, using it to escape his own handcuffs.
Whether you love Freddie Lounds or hate her, you have to admire her for staying calm and never losing her cool when she's kidnapped by Gideon, forced to watch him operate on Chilton and then keep Chilton alive by pumping air for him.
In the season finale, Alana finally figures out that Will is suffering from encephalitis when she hears him mention Lecter having him draw a clock, which prompts her to ask him to do it again and lets her see how distorted it is, meaning that Will has a physiological reason for his behavior. She looks ready to cry from relief and at that point the audience is too.
Though the context makes it rather painful, what with Will being incarcerated and Hannibal getting off scot-free, there is something undeniably awesome about the final scene of the finale: Will making it clear as crystal that he knows Hannibal is the killer and, to a lesser extent, that he's fucking pissed rather than afraid... and Hannibal smirking in vaguely triumphant amusement The scene can be seen as an evil Crowning Moment for Hannibal too, since it's incredible for a serial killer to successfully frame the investigator of his crimes for the killings.
Let's face it; there's a meta moment for the Hannibal fandom. The show was getting low ratings and in danger of being cancelled, but the fandom rose to the challenge and, through various ingenious and imaginative Twitter and Tumblr campaigns, managed to make the show one of the most talked about series of the year, ensuring its' renewal for a second season.
Plus, this is actually the first time Bryan Fuller has ever gotten to end a season of one of his shows on his own terms.
Crawford vs. Hannibal. Every move is perfectly choreographed and shot, giving us a strong contender for the greatest fight scene in TV history.
The most awesome part has to be the start when Hannibal throws a knife at Jack and embeds it in his hand. What does Jack do? He pulls out the knife and tries to stab Hannibal with it! Jack Crawford Took a Level in Badass there without question.
The first scene in "Kaiseki" with Will and Hannibal on screen together. Will is no longer the confused investigator of the last season, and he can actually see Hannibal for the villain that he is. What really makes it a Crowning Moment of Awesome is the Badass Boast at the end:
Will: I'm going to remember, Dr. Lecter. And when I do, there will be a reckoning.
Roland Umber, the man abducted by the eye-mural killer in "Kaiseki" wakes up and escapes at the start of the next episode, as his previous heroin usage gave him resistance to the deadly dose of opiates. After tearing his flesh pulling himself from the glue and stitches of the mural, Umber manages to smash the lock of the container holding him and run out. Of course the killer then sees Umber and hunts him through a forest and cornfield, with the victim doing well to avoid the killer's sight and rifle. Backed up against a high river cliff and facing the killer, he jumps off the edge, only just hitting the side and dying.
Will completely playing Hannibal by convincing him he no longer believes his own innocence.
Dr. Du Maurier, now suspecting Will is right about Hannibal, tells him she's quitting as his therapist, not showing any fear despite being alone with him as he advances towards her. And she actually does get out alive and even tells Will she believes him.
Will effortlessly deducing the nature of the finished eye mural just from looking at a picture. He quickly works out that Hannibal saw the man from the roof hole, then stitched in the murderer and took a leg as a trophy. Then he seamlessly pretends that he has no idea it was Hannibal who did it. Even Hannibal looks surprised with Will's speed. Best of all Will breaks out his catchphrase for the first time of Season 2: "This is my design". Then he eerily subverts it with "You are not my design," when he works out how Hannibal changed the mural.
Will's lawyer effortlessly undermines Freddie Lound's accusation against Will of being a murderer in the eyes of the jury by forcing her to admit in court that she's been sued for libel six times, and settled each time.
Bella Crawford, reeling from chemotherapy and having just been revived from a suicide attempt, summons every bit of strength left to her and slaps Hannibal across the face.
Will finally working out that Hannibal's a cannibal.
The fight scene in Hannibal's basement, even though it's brief and mostly off screen. Hannibal moves almost inhumanly fast to strike out the lights as Beverly shoots at him. The camera then pans up while several gun shots are heard, before finally a bullet goes up through the ceiling. It just works as a very effective sign that Hannibal got close enough to Beverly to force her arm up, and so she's now a goner.
Matthew Brown, with just a handy use of a tranquilizer dart, comes closer than anyone else probably ever will to killing Hannibal. He even gives Hannibal a verbal smack down for betraying Will and when the good doctor tries to turn him to his side, Matthew happily informs him that he doesn't care if Will's a murderer or not. Hannibal's usually composed face is a sight that has to be seen, if only for a few short moments.
On the topic of that scene: Hannibal is remarkably composed for someone who is probably going to die. He even gives a kind of Badass Boast to Brown when he is provoked.
Matthew: Maybe your murders will become my murders. I'll be the Chesapeake Ripper now.
Hannibal: Only if you eat me.
Crawford says he understands if Zeller and Price want time to grieve and don't want to examine Katz' remains, but Price is firm — "We're not running away from this, Jack. Beverly wouldn't."
Chilton deserves his own in "Futamono". He's the only person outside of Gideon and Will that accepts Hannibal Lecter is the Chesapeake Ripper, and repeatedly tries to convince Jack of this. Never once does he back down, despite Hannibal making not-so-subtle threats. It's pretty major character development for a man who was seen as little more than a greasy, sassy sleazeball in the first season.
Hate him or not, there is something that is both chilling and beautiful about the way Hannibal sets up Dr. Chilton in "Yakimono". It's obvious from the prep with Miriam Lass that he had been planning to execute such a plan for quite some time. Conditioning someone thus does not happen overnight. But he plays everything perfectly, and once he realizes Jack is having Miriam look at him through the one-way mirror at FBI headquarters, engineers everything so that Chilton will be next at that table. He doesn't even have to be there for the execution.
In "Su-zakana", Hannibal grabs Will's gun out of his hand as the latter prepares to fire, placing his thumb to block the hammer, while risking three of his fingers getting blown off.
In the same episode, Peter is severely emotionally traumatised as his social worker Clark Ingram released all of his animals and then killed a horse. He also possesses severe brain damage from a horse kick to the head. Yet he still manages to subdue Ingram despite being unarmed and his assailant wielding a hammer, knock him out, and then stitch Ingram into a horse. He wanted Ingram to feel the pain and trauma that Ingram inflicted on his victims.
The exact details aren't known yet, but the animalistic killer of "Shiizakana"? Who mauled at least three people? Was killed by Will Graham, with his bare hands.
Will has Randall at his mercy with a double barreled shotgun, then he chucks it away for intimacy's sake. Tier tries to crush Will's face in with his hydraulic cave bear skull suit, but Will traps the jaws up against the wall, lays him out with a bloody knuckled smack-down before breaking the bastard's neck. With his hands. All while hallucinating him as the Ravenstag, Hannibal himself and the Wendigo.
After we spend almost the entirety of "Ko no Mono" thinking Will killed and ate Freddie and has been seduced by Hannibal, the reveal that Freddie's alive and well and both she and Jack are in on Will's long con is pretty damn satisfying.
Will punching Mason Verger in the face, especially Verger's apparent confusion at what's happening. Will then calmly threatens to throw Mason to his own pigs, and then points a gun at Mason's head, before finally deciding it would be more fitting to have Mason kill Hannibal.
The show has been renewed for a third season — Fuller has broken his curse!
"Tome-wan" has quite a few:
Will telling Hannibal straight out about the above-mentioned stuff with Mason, along with an unintentional Ironic Echo (as he wasn't there to hear Hannibal say it the first time) that he was curious to see what would happen.
Jack revealing that he's even keeping Will in the dark about some parts of their plan to take down Hannibal, as after a great deal of effort he's managed to locate Dr. Du Maurier and get her safely into FBI custody.
Hannibal showing more of his fighting skills against Mason's goons, including a leg sweep a ninja would be proud of.
Carlo taking Hannibal down Matthew Brown style, by bringing a taser to a knife fight.
Will turning on Mason by freeing Hannibal, knowing it'll get him attacked, but still getting to see Hannibal make good on the opportunity before he passes out.
Hannibal making sure Mason pays in full for all he's done without killing him, so that Margot will still have access to the family's money. Namely, leaving him with half a face and quadriplegic.
Margot standing triumphantly over the helpless Mason, and declaring that she'll be giving him the exact same level of care he's given her all their lives.
Despite all of the advantages that Hannibal has in the episode, Will still manages to give him a brutal Wham Line that confirms just how much he has effected and changed Hannibal throughout their time together. Whether he wants to admit it or not, Will has managed to creep under the doctor's emotional walls and make him feel more than anybody else since Mischa, including hurting him with an inevitable betrayal. Hannibal doesn't deny it.
Hannibal: Did you think you could transform me?
Will: I already did.
After being manipulated by Hannibal for most of the second season, Alana finally gets the opportunity to confront Hannibal and she doesn't hesitate to point a gun at him, especially after discovering that Jack was trapped and injured in the pantry. If Hannibal hadn't removed the bullets ahead of time, there's no doubt that Alana would have shot him dead right there in his own blood soaked kitchen.