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Nightmare Fuel: The Amazing Spider-Man
For those who are arachnophobes, the scene where Peter first steps into the room in Oscorp with all of the spiders and accidentally activates something that ends up dropping several spiders all over him. Even scarier knowing that one of those spiders later bit him and then was eventually found to still be crawling around on him. Not to mention all the closeup photos of big hairy spiders during Peter's internet research. And the pictures of spider bites.
The lizard-mouse's ultimate form. We see it, half-lizard, eating its fellow mouse and twice its original size, with the hind legs and mouth of a lizard.
The Lizard himself is quite scary. A noteworthy moment being when a transforming Connors enters a taxi to head for the same place as the Oscorp agent and the driver asks if he's alright, to which Conners responds in a deep, growling tone:
Perhaps the creepiest quote by the Lizard is when he confronts Peter at his own high school.
"Nowhere to hide, Peter!"
What makes it creepy is just how.... "normal" it sounds. No real baritones or growling. It sounds almost completely like it's pre-transformation Curt Connors speaking. This vocal dissonance plus the Slasher Smile he's wearing as he says it in that playfully mocking tone just makes it all the more unnerving.
The scene in which Peter has spun a web to see if he could track the Lizard in the sewers. We see a huge shadow, thinking it's the Lizard, when it turns out to be just a common lizard. Then we see a larger tail drop behind Peter...
When Gwen is hiding in the closet from The Lizard. The Scare Chord does not help matters.
The bridge scene, with all of the panicked citizens running from The Lizard. Then there's the child that Spider Man had to save... it was scary to almost see that child die. It also shows that these are normal people who are being affected by the events of the movie. Unlike in most other Spider-Man media, we see these events as actual tragedies rather then just Fan Wank moments of awesome action. It's also the first time we, albeit subtly, get an insight into Peter's relation with the normal everyday citizens of New York, and his feelings about saving normal strangers lives.
In the deleted scenes, there is a sequence that ends with the death of Dr. Ratha in which the Lizard is implied to bite his head off.
The Cross Species Rampage at the begining of the game, with Scorpian, Rhino, Nattie, Vermin and Iguana, attacking the Oscorp scientists. Doesn't help that as the rampage starts, Vermin bites Gwen's arm infront of Peter, while Peter, and yes, it was a POV shot.
The cross species virus itself, Smythe sums it up best.
Smythe: Any direct contact with these things lead to infection; infection leads to death, or becoming a cross species yourself.
And there's the Infected, which are basically humans taken into the sewers, becoming zombie-like animalistic ceratures. Turns to Fridge Horror when you realize that these are probebly innocent people with their lives ahead of them.
During the climax, we see New York is basically a warzone; people are walking around, likely on the verse of transformation, and the infected are loose on the streets to, but are restrained by metal fences from attacking Spiderman, and there are Smythe's robots going rampet, set to kill the infected citizens, and Smythe personally operating a giant robot that is constantly firing missles. Basically it's like the end of days.