- A stock example for this franchise is the plot point that cybernetically-enhanced people's brains can be hacked by various parties for various purposes, doing things ranging from messing with their vision to allow someone to be kidnapped in the middle of a crowded street without witnesses, to giving them false memories, or even forcing them to commit suicide or murder. Or, in a funnier abuse of this technique, for the Major to make Batou punch himself in the face.
- The episode "Jungle Cruise". A Serial Killer who skins his victims alive and leaves them in great pain to die a while after it? Check. Showing the victims in all the gory detail? Check. Showing a video of the killer beginning to skin his victims alive, including a scream which consisted of pure blood-chilling agony? Check. This particular episode was gruesome enough to get an extra Content Warning on [adult swim] (and some light editing, mostly muting out "shit" and "dickhead"note and digitally darkening the scene of the first murder so the viewer can't see the female victim's breasts). On Canada's YTV, the episode was initially banned due to brutal content, though the episode did eventually air with a similar warning to [adult swim]'s stating that the episode's violence is beyond what YTV usually allows.
- The scene which best exemplifies the episode is when Togusa is watching the video of the woman about to be skinned alive, and just as we hear the bloodcurdling scream, he runs outside nearly throwing up. Nothing Is Scarier indeed.
- The killer also plugs into his victim's brains to make them see through his eyes. He makes them watch themselves being skinned alive.
- Somewhere it had been admitted that this episode was a homage to the film Strange Days, and rightfully so, only what happens here is a touch more horrific.
- "Not Equal" features Section Nine investigating a heiress of a cybernetics corporation that had been kidnapped a good number of years ago by terrorists opposed to cybernetics, due to the fact that she appeared seemingly unaged and in charge of them in a recent report. In reality, an old woman found alongside her that is attempting to commit suicide turns out to of been the original girl given the one-of-a-kind cybernetics in her that the younger one lacks; the reaction of one of the JSDF soldiers that linked into her mind being a Despair Event Horizon and the circumstances all but state that the terrorists raped the girl enough to break her and made her daughter their new leader just to mock her. Her being an old woman was from the sheer physical and mental stress she'd endured causing her body to age rapidly.
- The manga version of the story turns it from heavily implied to an outright confirmation, though it does ever-so-slightly mitigate it by having the heiress raise her child to be able to fend for herself.
- The season one episode "Eraser" has Section 9 facing off with a corrupt narc squad attempting to cover up a conspiracy. When the enemy brings out a Powered Armor, even Motoko doesn't stand a chance in a one-on-one encounter and gets her left arm blown off before being stomped into the pavement. What follows after Saito manages to save her at the last second is one of the few times in the franchise the Major gets absolutely livid, blasting the pilot's cockpit with an anti-armor rifle over and over with only one arm until he nearly suffocates to death out of raw payback. Don't fuck with the Major.
- The following episode has the enemy respond in kind by drugging and attempting to frame the Chief for drug usage, and one of their agents slips into handling Motoko's body swap procedure when she needed to get out of her still-damaged body. Which they promptly abuse to stick needles in her brain to screw with her cerebral sensory, all the while mocking her about it and her inability to prevent it. It takes a Big Damn Heroes from the Laughing Man himself to save her, and Motoko thankfully gets some payback by roundhousing the agent clean through a thick glass window right after their massive Oh, Crap! at realizing the needles had been removed.
- The Laughing Man is a major, integral part of season one's storyline as the acting influence that stirs the entire plot into motion, both in the past and present even if the individual responsible for the 'Laughing Man' caused it unintentionally. But then there's the revelation that spooks even him to that day: the data he acted on before confronting Serano just.. appeared to him one day from an anonymous source, and despite his best efforts, he never found out where it came from. Whether it was an anonymous benefactor looking to expose the truth as well, a competitor out to shut down Serano, or otherwise is not even remotely given any ounce of an answer, meaning the entire plot occurred because of a freak circumstance no one had an answer for.
- Worse yet, the Laughing Man intended to uproot a corrupt series of events that endangered many lives. Instead, The Conspiracy intentionally angled his abduction of Serano with a trumped up ransom charge and created the Laughing Man as a false spin while blackmailing Serano and making a killing in manipulating the stocks and profit all along the way. In a strong case of Nice Job Breaking It, Hero!, the original Laughing Man accidentally created an in-universe Memetic Mutation that would blow up in everyone's faces while giving the Greater-Scope Villain of the arc the perfect excuses to consolidate their power high up within Japan's government. Considering what follows is an attempt to Kill 'Em All against Section 9, it's downright terrifying how close a Near-Villain Victory occurs thanks to their excessive machinations in everything.
- The first time the Individual Eleven assemble they cut each other's heads off live on TV, save Kuze.
- There's also the time the Major fires an anti-tank gun into an armoured suit from point-blank while the guy inside is screaming in terror, though that's unintentionally creepy.
- Kazundo Gohda. Period. Also, the last episode of 2nd Gi G when Section 9 attempts to capture Gohda, only for Major Kusanagi to BRUTALLY kill him (you see his head explode, leaving only his lower jaw and tongue).
- The second series uses exploding heads symbolically, once in the first episode and once in the last. There is no panning away.
- The manga manages to give Batou a genuinely scary "Rape Face◊" in it's portrayal of episode 7: "IDOLATOR"
Nightmare Fuel / Ghost in the Shell: Stand Alone Complex