The creepier part is that you can now clearly see that the little things protruding from Lilith's lower area look like human legs. They even shake around a bit.
This◊ version of the deformed Rei in Rebuild. It does not help matters that it brings back memories of the Giant Naked Rei/Lilith from End of Evangelion.
The first quarter of Rebuild copies the first few episodes nearly scene-for-scene, and it's all very familiar... until the Sixth Angel, Ramiel, shows up. Now it's this morphing, singing monstrosity that screams inhumanly as it tries to melt EVA-01's face off. Okay, feeling the impact again. Not to mention that, while the officers are discussing a change of tactics, Shinji is continuously screaming in pain because Ramiel's laser is still boiling him alive.
And the fact that he begs Gendou to rescue him while said 'father' continues giving orders coldly, completely ignores him and is actually the one responsible for this — almost as if he were torturing him to death.
Ramiel itself is a very weird combination of Awesome and Nightmare Fuel. Out of all the Angels, you'd probably be most forgiven for thinking Ramiel a machine of some kind. Nothing about it looks organic, and the efficient, methodical approach it takes in dealing with threats just reinforces the idea. Then it gets hit with the Positron Cannon and screams, shifts into a starburst pattern as though flinching from the pain, and pours hundreds of gallons of blood all over the landscape. That's when you realize: this utterly inhuman and otherworldly thing is actually alive. This makes Ramiel a lot scarier than if it were simply a machine.
Not to mention that when Shinji goes to rescue Rei from the core, the Angel gunk inside it is basically burning him alive to the point that his skin peels off.
Unit 02's berserker state, seen earlier in the battle, is pretty crazed as well. Watching a Humongous Mecha turn into something that resembles Carnage from Spider-Man (complete with gaping mouth, needle-thin teeth, and lolling tongue) and going medieval on Zeruel much have been quite a startling sight to see on the big screen.
That has got precisely nothing on the pilot's, Mari's, face. Dear Lord, this troper didn't sleep for days. Although being said, pretty much anything that happened in that scene was 3000% raw terror.
Unit 03's destruction. The original scene was already fairly gory and many kinds of disturbing, but Rebuild adds in Unit 01 eviscerating it, in all its gorny detail. And—rather than being crushed—the entry plug is bitten in half, and we hear Asuka's agonized scream (it comes a fraction of a second before Shinji's Big "NO!" and is too high-pitched to be him).
It certainly doesn't help that this song is playing through the whole scene.
Another scary part is the build-up to the scene, where we see Toji acting suspicious, similar to in the original series, and watchers of the old series think that the scene is going to repeat itself with Toji being the pilot of Unit 3. Then, when Asuka is named the pilot, it lures the old fans into a sense of "oh, they aren't going to copy the original series" and then the entry plug slowly turns blood red... When this troper watched the movie for the first time, he was totally fine until the sudden mood shift.
Remember the robotic sounds as the Dummy System starts up? Well, listen to it playing backwards, and you'll hear words. English words. "Freedom is an illusion. All you lose is the emotion of pride. To be dominated by me is not as bad for humankind as to be dominated by others of your species."
Of note: The Dummy Plug System activating now resembles nothing so much within the entry plug as an Angel itself, rising from behind to just bend over and stare directly into the Pilot's face...
The added gruesomeness of the scene is in universe treated as Nightmare Fuel in both reiterations, but here Rei goes for a look (the Dummy System is based off her) and she is shocked and appalled. Even Rei is squicked.
As in the series, 01 refuses the Dummy Plug and for one brief, fleeting instant, you can hear an almost human, agonized scream as it's rejected.
There are two separate incidents where an Eva pilot's synchro rate goes too high, followed by Ritsuko proclaiming that they need to remove the pilot immediately, because if they remain in that state, they "won't be human anymore".
The very fact that as of the end of 2.0, everything is still going according to Gendo's plan.
When the 8th Angel (that new eyeball one) was about to fall onto Unit 01, these human-looking things on its arm sprung up and danced. Just...look◊.
New Angel? Oh, silly. That's Sahaquiel. That is Sahaquiel. It speaks volumes for both the Angel redesigns and Rebuild as a whole that an Angel previously thought of as one of the weaker foes was made genuinely terrifying.
Plus, the violins of hell, drums of the damned, and Satan's orchestra singing in Latin gave life to the scene while at the SAME TIME adding to the terror of it all!
The Evangelion Simulator is practically a trashed EVA-prototype with only a spine and head, and even then its head is cracked open. The very thing is a monstrosity.
The scene featuring Zeruel, and people fleeing into the Geofront Shelter. Not too bad, but for a brief second you hear a child crying. A small but brilliantly effective moment.
Near the end of 2.0, when Shinji is trying to save Rei after being eaten by the angel, it closes up on the core, focusing on tiny little cells, that look almost like tiny Rei-heads. It may be my eyes, but Christ.
They are tiny Rei-heads, and at one point they start talking to Shinji with Voice of the Legion!
A possibly fan-specific example. There are two new versions of "Komm Susser Tod" out, both of which begin with a One-Woman Wail. The Dubstep version is also freaky as hell.
Find out that in 3.0 that most of humanity died due to Shinji's actions at the end of 2.0.
Just the shot of the fissure that's lined with enormous red human teeth. No it's not just a case of a certain infamous male fear, it's the fact that this fissure is probably large enough to be visible from space. That's right, Third Impact gave the planet a freaking mouth. And it seems like this was a work in progress. Just what will the world look like when it's finished? Do weeven wantto know?
There's a very good hint in the previous film. Pay attention to Unit 01's mouth when it Awakens at the end of 2.22. Do those teeth look familiar?
The possibility of a Fourth Impact
As of the end of 3.0, the possibility of Fifth Impact; a.k.a. FINAL IMPACT
At one point in 3.0., Shinji and Fuyutsuki are playing Shogi in a pitch black room. Cue Fuyutsuki telling Shinji about Rei's origins, and then he turns the lights in the room on. What do we see? Dozens of severed Rei heads lined up on the wall behind him.
When Shinji and Kaworu descend to Terminal Dogma, we see that countless gaping skulls cover the floor now. And let's not even get into Lilith's decayed husk...
Kaworu unfortunately has to sacrifice himself to stop Fourth Impact. How does he die? He explodes. Right in front of Shinji, and bits of him and blood are plastered on the walls of the double entry plug. Try to imagine yourself as Shinji, unable to act, watching as your friend just blows up in front of you.
That whole thing with the pilots being stuck in 14-year old bodies. It's an unnatural, physical, irreversible consequence of them tampering with Gods, they're never gonna find partners, and then there's the factor of what this means for their mental states and developement.
Shinji's Situation in 3.0. Imagine waking up to find that everyone in the world, including the closest thing you had to a parent, hates you. It gets WORSE.
When Shinji is retrieved from Eva-01, the way they refer to him first is as "Test Subject BM-03", he is no longer considered as a human being.
Eva-13's transformation into the instigator of Fourth Impact. Which has the Twelfth Angel be a giant creepy Rei head before turning completely into a core that Eva-13 devours.
Asuka and Kaworu begging Shinji not to release the spears and him doing it anyway.
What? No mention of the giant, decaying Rei's head in the NERV headquarters and the further Body Horror it goes through as the Fourth Impact starts?
From a psychological standpoint, the multiple revelations Fuyutsuki gives Shinji, including a brief shot of an angelic-looking Yui with tubes coming out of her.
The so-called failed moments/aspects (depending on translation) of infinity. Yes, they're giant, and they look like Evas, but they're indistinct. Mass-Produced Evas? A strong possibility, but there are thousands, if not *millions* of them, forming spires and city-blanketing masses. Nerve and Seele never had those resources, especially not post-third-impact. You know what there were millions of? People. Who aren't around any more. Then, FOURTH Impact starts, and the shapes begin getting blown around in the wind/wonky gravity, and they're noticeably less like Evas...
The landscape. Look at the red parts very closely. There's a pattern swirling around beneath the surface. The same one associated with cores, as a matter of fact. Everything has been turned into core material! Eva 13 starts turning Unit 08's arms into core as well.
Shinji's mental breakdown about two-thirds into 3.0 is terrifying. One dreads to think of what it was like seeing it in a theater - the background is rendered in an Uncanny Valley-inducing, realistic way. The background starts to sway and spin dizzily as Shinji sways uneasily in time with it, his pupils vanishing. The scene then Jump Cuts to Shinji alone in his room, realising that a) Rei as he knows her is dead, and b) HE KILLED EVERYONE.
At the climax of Fourth Impact we are treated to an unimpeded view of the tear in the fabric of reality that is the Door of Guf. Floating in the black void beyond, there is what looks like a glowing black hole speared by six long tesseracts slowly being pulled towards the Door of Guf. We see the object looming ever closer as the portal closes. What the hell was that thing? Even scarier, what would have happened if it had reached Earth?
If you thought Shinji's situation was already horrible by the end of 3.33, then what awaits for him in 4.0. Not only did he lost his last friend in a rather gruesome way, he's already tormented by the guilt of killing the whole world and nearly repeating the deed and most of the people that remain are shown to have a strong hatred or grudge at him.
The Rei that Shinji came to know and care about, the one he saved? She isn't in the movie. As far as Shinji can tell, she doesn't exist anymore. He accidentally destroyed the world, and the person he did it to save doesn't even exist. And walking around, wearing her face but having none of her identity or personality, is her clone. It's harder to say if Shinji or the audience found this more horrifying.