- The two-part story of the machine/human war - The Second Renaissance - is particularly brutal. A gynoid is beaten to death by a crowd of human men. She is beaten, stripped of her clothes and eventually of her synthetic skin, revealing her robot body. All the while she screams, her voice becoming more machine-like with each blow. What makes that scene a lot worse is what the woman is screaming: "I'm REAL!"
- The rest of that sequence is no less disturbing in its imagery. Some choice selections include; a Tiananmen Square gone wrong in which a robot is graphically crushed beneath tank treads; seemingly thousands of robot corpses, so many it takes giant bulldozers to move them around, being shovelled into mass graves; scenes of rioting robots being gunned down as they surrender or (as mentioned below) shot in the head at point blank range while handcuffed. What makes it worse and all the more reminiscent of real-world horrors is how human nearly all of the victims appear.
- The scene of the millionaire having her head crushed by her once-peaceful robot servant B1-66ER.
- As well, the scenes of what else B1-66ER had done before that (stomped her dogs to death and murdered various other people).
- There was the battle scene where a soldier has the front of his mecha unit ripped open by a Sentinel robot, which coils its tentacles around his torso and rips him out, leaving his arms and legs strapped into the mecha. The worst part is way the man is screaming "God help me! GOD HELP ME!!!" right up to the last moment.
Instructor: Then man made the machine in his own likeness.
- Heck, everything about the war is horrific - it's viscerally presented and unblinking in its portrayal about how pants-shittingly terrifying and violent it was.
- The whole sequence is disturbing in its implications of the machines, namely their rapid evolution from humanoid designs to completely alien forms and their ability to shrug off multiple nuclear strikes mid-battle, but the power armour removal scene sticks out in particular. They could've stuck one of those tentacles through his head, blasted him with a laser, something quick and efficient as a machine would do; instead, they rip him limb from limb, seemingly purely because they were in a position to do so. The machines are now capable - perhaps even fond - of cruelty. Given what they go through at the hands of humanity, and that they are distinctly noted as being artificially intelligent (IE, capable of learning and complex thought) it isn't surprising in the least. After all, humans did create the machines to be like them.
- The last scenes where Prisoners of War are being surgically operated and experimented on by machines while awake.
- As well as being entombed into the power plants, being violently plugged and staying there in agony for the rest of their lives. As the Matrix wiki puts it, "the first captives suffered in pain and horror enroute to what the machines viewed as the human's version of a 'perfect world'", and the visuals and painful moaning don't lie at all.
- All the disturbing imagery in The Second Renaissance is made even worse when you learn that most of it is based on real-life occurrences. For instance, there is a sequence where a human soldier shoots a restrained and helpless robot in the head point-blank with a pistol. Sound familiar?
- One the worst parts was that - judging by the obvious bias in the supposed "historical record" - the Machines are just as prone to arrogance, self-righteousness, and all the other human failings as we are. It's like the human race quadrupled in capacity for terror, Three Laws be damned! The other option is that preserving the human race in the pods is actually the Machines' idea of keeping the human race safe...
- There was a short about a track-star who almost, almost managed to break out of the Matrix... But at the last moment his muscles snapped, confining him to a wheelchair in a catatonic state. We're never told if the Agents had something to do with it (they were aware of him) or if it was simple human failing, but it was possibly the most haunting entry in the anthology, and the realistic-yet-exaggerated animation didn't help. The short ends with him trying to get up again despite being wheelchair-bound; he almost succeeded, but falls down again.
- Everything related to humanity's current state, the cloning farms, the VR prison system, army's of robotic killing machines scouring the tunnels for escapees, isn't just deserved/a reasonable response in the aftermath of the war, but exists due to a massive act of mercy on behalf of the victorious AI civilization, exists solely to ensure humanity can never threaten to annihilate them again without sinking to their/our level of depravity and outright genociding them.
- The big, black nothingness encountered by Yoko in the hounted house. There is nothing there. Literally. A seemingly endless void caused by a series of glitches right behind generic doors. While compared to things shown in other segments, it's just some random error in the simulation, but by itself it's downright horrific in otherwise calm and harmless segment.
- Duo. Not as a person, but his role. Since he's nothing more but part of a training program, it means the same training program is capable of entirely messing with Cis' emotions and feelings. Just recall how she jokes about Duo finally proposing to her when the simulation starts and how utterly devastated she is when forced to kill Duo. It is never fully explained if Duo is fully a fabrication or was based on Cis' real partner, but the sole possibility of him being pure fiction and a relatively minor program being capable of making Cis feel love toward him - even after the test is over - is mind-numbing.
- There is even worse option. Duo is a real person and the training forced Cis into killing her beloved one, being convinced that this is a real situation and not a set-up. Now that makes not only her ordeal even more painful, but also paints the people who created and put her through such test as unscrupulous bastards, openly toying with her emotions.
Nightmare Fuel / The Animatrix
The Animatrix, a series of animated shorts based on The Matrix trilogy, not only had some quite disturbing material, but half of it couldn't even be understood unless you were crazy or an art major. Spoilers below.