The fact that the process that mutated him was killing him.
Batman electrocuting Metamorpho.
"Wayne hooked. Awaiting instructions."
Lady Shiva using the Soultaker Sword on Dr. Ravencroft onscreen. The end result is horrifying, to say the least. What really makes it chilling is Ravencroft's screams as Batman and Tatsu look on in horror.
And the only reason she doesn't use the sword on Silver Monkey? She's got something worse in mind for him.
When Barbara gets kidnapped by Phosphorus Rex, we get a POV shot of her terrified face as she's grabbed.
The Ghosts in general. They never say anything aside from a few grunts during combat, their general appearance is quite scary, and then there's the way they emerge from the shadows after Match calls for them.
Pretty much everything about Cypher. He's very stealthy and often crawls on the walls, can make you into his personal puppet with his tendrils, and judging by what happened with his first victim, being his puppet isn't very pretty. Not to mention that when he talks through his victims, it's in their voice mixed with his own, complete with creepy metallic echo. And when he laughs, it's terrifying. Especially when he's talking through his victims.
Jason Burr still being under control in the episode's end.
Anarky's plan to unleash a Titan-esque virus on all of Gotham. Not to mention when we see the virus' effect on the two ninjas.
The sight of Ra's al Ghul in a cryogenic suspension unit.
Tatsu getting infected from the virus.
Pyg and Toad's deathtraps.
Jason Burr: Don't worry. She doesn't suspect a thing. By the time she and Wayne know what's happening, the Ion Cortex will be complete and in your hands.
Lady Shiva: You will be generously rewarded for your assistance, Dr. Burr. Welcome to the League of Assassins.
Magpie's sanity seems to have deteriorated even more since her capture. Even worse, she's gone full-blown Yandere for Batman and nearly kills Katana by burying her alive in a coffin.
The League now has control over Gotham's electricity network, and they've taken Batman prisoner.
You thought Dr. Ravencroft's fate was unnerving? Well, it happens again, and this time, with Jason Burr, a major recurring character as well as Katana's sort-of love interest. Way to come into your own, Beware the Batman.
Ra's al Ghul's defeat: Being dragged down an elevator shaft by the ghosts of his past enemies. That were imprisoned in the Soultaker Sword
The ending of this episode is quite chilling, as Batman, becoming increasingly ruthless due to Alfred's abscence, breaks down training boards aggressively as a concerned Tatsu tries to call Alfred on the phone and begs him to come back home. The editing, sound, and voice acting really sell it.
The beginning of the episode. Full stop. To elaborate, armored thugs have broken in to a store only to be picked off one by one by a mysterious assailant. At first, you're thinking it's probably Batman, but when we get a closer look at him, it looks nothing like Bats. The assailant takes down the thugs and you're left wondering "What the hell is that thing?" thanfully it's revealed that it's Metamorpho who is trying to protect Gotham.
The very idea of armored thugs intimidating store owners into leaving Old Gotham. For a comparison, think about the Mafia and their extortion racket. Made even scarier by the fact that it was orchestrated by Stagg's daughter. It seems the apple doesn't fall very far from the tree.
Bruce's Crime Alley flashback, particularly when the way Martha Wayne was shot heavily implies she was shot straight in the head for young Bruce to see.
Humpty Dumpty's back, ladies and gentleman. And he's more terrifying than before. The episode can best be described as a twisted, G-Rated Shout-Out to the Saw franchise.
After Batman and Katana meet up with the others, Humpty reveals himself and orders them to open the tray on the table, revealing that it was a dead body. The horror is lessened when it's revealed it's just a manniquen, but Goddamn. What Do You Mean, It's for Kids?
Let's run through Humpty's deathtraps:
When Batman and Katana meet, the room they're in has a pendulum, acid, and flames.
Marion Grange gets trapped in an air-tight egg-shaped prison. She only had two minutes before she lost all of her oxygen and would have died had Batman and Katana not solved the riddle.
The next room had lit floor tiles that would give out when they darkened, causing anyone who stood on them to fall.
Another room was filled with spikes.
Hell, Humpty in general was a walking tank of Nightmare Fuel. While he was scary in his debut, he was still sympathetic, but here? He's a full-on sadistic psychopath.
Seeing Marion Grange, a stoicIron Lady, freak out over the course of the episode was truly frightening. In fact, the experience so thouroughly traumatised her that the next episode revealed she had to take a vacation, and later she resigned.
And there's the fact that an innocent man got sent to jail for a crime he didn't committ. Made scarier by the fact that this actually happens in real life!
Hell, it was so frightening that it even scared the goddamn Batman! The same Batman who regularly beats up thugs like it's Tuesday. Let that sink in a moment.
When Katana walks in just as it was happening, Batman's response really hammers it home.
Batman: Go away, Katana. You shouldn't be here. You shouldn't see this.
The opening of the episode has Bruce having a nightmare about his battle with Killer Croc and confessing to Alfred that he's afraid of losing control of his Batman persona. It's really unsettling to see The Batman genuinely frightened by something and makes Magpie's Not So Different speech in Attraction a lot Harsher in Hindsight.
Professor Pyg shows that despite being considerably toned down in comparison to his comic counterpart, he still retains his Mad Scientist traits. His plan in this episode? Create an army of Human/Animal hybrids with a special serum. And his first victims are three frightened women. Thankfully Batman and Katana free the women before they could start.
Pyg was even willing to let Mr. Toad pick one of the women for a bride.
Killer Croc is shown to be a cannibal, unlike most animated depictions, when he tries to eat Barbara Gordon. He also continuously calls her "girlie" and "sweetie", which makes his hunt for her even creepier.
A deranged, disfigured Harvey Dent stalking and threatening Jocelyn Kilroy and newly-appointed mayor David Hull to do his bidding. The former's POV is pretty much filmed like a horror film, and the later is unsettling considering how Hull was playing him along and dismissing him earlier in the episode.