- Human harvest!
- The interrogation scene (pictured) when Agent Smith makes Neo's mouth melt itself shut, causing him to panic understandably to where they shoot in the tracking bug.Agent Smith: Tell me...what good is a phone call when you are unable to speak?
- Neo himself thought it was a nightmare. When Trinity sucks out the "bug," his reaction is "Jesus Christ, that thing's real?!?"
- If you're someone that has a fear of insects or other creepy crawlies, then this scene would just get worse and worse as the tracking bug is literally and figuratively a centipede-like bug, that comes to life from the click of a button and just uses its tendrils to squirm and crawl into Neo through his exposed navel, his sealed mouth blocking his presumed screams of pain (as one can see the tendrils poking and squirming around his belly).
- Agents in general are terrifying. Implacable, inhumanly powerful, and capable of possessing and overriding anyone still plugged into the Matrix. This last bit, we get to see several times throughout the franchise, watching various people in various outfits morph gruesomely into a man in a nondescript suit and sunglasses, regardless of whether or not they were a man before, or for that matter wearing sunglasses. And in the rare instance when someone manages to kill an Agent, they release control just before the body dies, leaving the human they were behind. Most of the time it's a cop or security guard, but on at least one occasion we see a lady who just got back from grocery shopping get taken over, right before that Agent gets taken over by Agent Smith.
- Neo's first entry into the real world. Oh, don't tell me you weren't horrified. And then the explanation of how it works...and how humans are fed...and how people jack in to the Matrix...and did we mention that our bodies could be taken over by evil unstoppable programs at any second?
- Speaking of Agent possession, during the scene when the Agents are chasing down Neo, there's a little Asian girl who watches what was probably her mom...suddenly turn into some guy in a suit and sunglasses. The people that Agents assimilate are somebody's loved ones and they could possibly get killed in brutal ways by a Zion operative.
- What about that part just before Neo fully wakes up? Yes, it's obvious they're pulling him out when he took the red pill and they've put him in a chair to get ready for it, but then comes that incredibly freaky part where Morpheus points at a mirror that just repaired itself, and when Neo reaches out to touch it...it turns gooey and starts to assimilate his entire body. And THEN, he starts screaming like all hell and you can hear it like the sound is glitching out; AND the camera goes down his totally engulfed throat. Metaphor or otherwise, who else was scared out of the room by that scene alone?
- The dèjá vu scene. The moment Neo points out what he just saw, the entire group freezes in their tracks. It's not clear (at first) what changed during the glitch, but it's definitely clear that something has just Gone Horribly Wrong. Namely, that the windows and doors have been blocked by brick walls and Agents are on their way.
- The Sentinels. They're giant mechanical monsters whose only purpose is to hunt and kill humans. They can't be reasoned with, their attacks can't be stopped, and they are very hard to destroy. It's even worse in Reloaded when we see thousands of them drilling to Zion - they look like huge bugs crawling around a gigantic hive.
- "He's gonna pop!" can be quite scary for any emetophobes. Rumour has it that this wasn't actually in the script, Keanu Reeves just had food poisoning.
Nightmare Fuel / The Matrix