[[caption-width-right:311:Excuse me, can I borrow some chapstick?]]
* Human harvest!
* The Matrix's second Beta phase- the Nightmare Matrix. It was created after the failure of the Paradise Matrix and, in sheer contrast to it, was designed to appeal to the sadistic side of human nature. It was populated with various monsters such as vampires and werewolves and wars were constantly raging. Despite the introduction of a cause-and-effect option, humans were still unable to make choices. [[AndIMustScream Imagine being trapped in a nightmare where you're forced to live out the events of a horror movie, with no control of your own actions, and even though you're aware the world isn't real, you can't wake up.]] No wonder it failed.
* In the Animatrix short ''The Second Renaissance'', an android woman is beaten to death by a crowd of men. They tear off her clothes and beat the fake human skin off of her while her screams turn into a mechanical bleating.
** Android lady's last words? "Please, no! No! I'm real! I'm re-"
** In the same short, the depiction of the forced extraction of a certain trooper from his powered armor. To give you some idea, he's [[spoiler:torn from the armor by a machine tentacle wrapped around his waist. His arms and legs, however, remain locked in the armor. And he's screaming in pain and terror the whole time.]]
** The scene in which a robot grabs a man's face and TEARS HIS SKULL IN HALF TO REVEAL HIS BRAIN. The brain then turns into some sort of diagram for the next scene.
* The interrogation scene (pictured) when Agent Smith makes [[AndIMustScream 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'''?!?"
* Giant flying baby face made of bugs. Egads.
* Neo's first entry into the real world in ''Film/TheMatrix''. Oh, ''don't'' tell me you weren't horrified. And then the explanation of how it works...[[ImAHumanitarian and how humans are fed]]...and how people jack in to the Matrix...[[ParanoiaFuel 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.
* The [[AGlitchInTheMatrix dèjá vu scene]] in the first movie. 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 GoneHorriblyWrong. Namely, that the windows and doors have been blocked by brick walls and Agents are on their way.
* The way Smith reveals that he assimilated Sati: ''"Cookies need love like everything else."''
* "There are levels of survival we are prepared to accept." Zion has always been in danger, but this is the first time it becomes clear that the ''entire'' human race has no secure stake in this world, and its continued existence has hung on the mercy of the Machines.
* 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.