For a mostly light-hearted Saturday-Morning Cartoon, this show (based on the movie of the same name) has more than its fair share of frightening alien monsters and villains.
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- The Skraaldians from the pilot episode ("The Long Goodbye Syndrome") end up being Paranoia Fuel up to eleven. They're a shelled slug-like race that comes to Earth to multiply, as they like the warm climate in the sewers. However, if any single one of them is killed, the victim will vomit on the killer. The vomit then permanently marks the killer down to their DNA as a target of revenge for the entire race, due to them being a psychically-linked Hive Mind. Worse, they can hide in the bodies of other aliens as parasites and burst from their chests to get to their victim, and masquerade as something as innocent as a human hot dog vendor before they strike. If you kill two or more, they will slowly put you in a large vat of soup at temperatures of 3000 to 4000 degrees to melt. They're so bad that Kay was willing to get stung by one, swelling up and turning the color of rotten eggplant for a week, just to avoid their wrath. As Kay describes to Agent J after he killed one of them:Kay: "Skraaldians possess a hive mentality. They're psychically linked. They saw what you did. They know what you look like. They know where you live. All of them... listen, Slick. This is a whole planet of dudes dedicated to your demise. Four billion assassins locked onto your DNA, thinking about you every three seconds."
- Kay managed to get Jay out of the Skraaldians' hit-list by hiring an Arquillian (who was piloting a robot suit decoy that looked like Kay, blowing his nose to draw the Skraaldians to himself), but if he hadn't Jay (and potentially Kay if he tried to defend Jay) would have been dead men for certain.
- Also, Jay has no idea that the "Kay" the aliens captured is a decoy - as far as he knew at the time, Kay was dead because of his mistake.
- During the episode "The Buzzard Syndrome" which introduces Buzzard, there's also the creature known as Z-Ron. While Buzzard himself is rather creepy (being extremely tall, pale-skinned, deep-voiced, wears a black coat to disguise his inhuman body) and proves that he's not a good guy (he tries to kill Agent K to keep him from interfering with Buzzard's bounty-hunt), his target turns out to be much worse. Z-Ron is a (literally) predatory, savage, vicious Serial Killer who travels around space to kill and eat other sapient aliens; he initially resembles a "harmless" teddy bear to lure his victims into a false sense of security before turning into a hideous monster to attack them, with L comparing it to a cat playing with it's prey. His spaceship is filled with about a dozen different alien skeletons, and decides sometime to add humans to his menu — he tries to hunt a young boy (by befriending and playing with him first) and later fools Agent J as well, chasing them both through a forest. This sadistic monster is definitely one of the nastiest one-time villains in the series.
- The antagonist of "The Psychic Link Syndrome" is Forbus, a mentally disturbed alien of the Alcidian race. Considered to be weird and socially reclusive even by his own species, he has an irrational phobia of cameras. Several unlucky humans who try to take photos or films of him find out the hard way about pissing off this guy, who decides to attack them and drains them of vital bodily fluids (his first victim turns so emaciated and shriveled-up that he resembles a corpse). Though fortunately, none of those humans died and they later fully recovered in the MIB hospital.
- There's also what Forbus does to Agent K; he grabs hold of him and establishes a Psychic Link, which forces K to feel every sensation (both mental and physical) that Forbus feels as well. Whenever Forbus is injured, Kay feels the same pain, and vice versa. Kay is also sharing Forbus' warped emotions and thoughts, until he turns evil and starts fighting Jay and Elle.
- The Psychic Link also means that whatever happens to Forbes will also happen to Kay, which becomes very problematic when the alien ends up in a showdown with normal police. Jay has to rush in to prevent the police from shooting Forbes, which would also kill Kay. Later when Kay fights the mind control and shoots the alien, both are seriously injured - Elle's reaction suggest that they almost died.
- There's also how Forbus first shows how the link works; he grabs the radiator of a car and forces K to feel the pain.
- The scene where the Astro-Tots seem to vaporize Kay. Jay has to watch the confrontation through the MIB communicator video, too far away to help.J: You took down my partner!
- The Nrak from "The Bad Seed Syndrome". They are a bunch of tiny parasitic spores that spread everywhere and infect people, brainwashing (and eventually transforming) them into new additions to their hive mind.
- Agent Alpha, a renegade MIB officer who decided that he wanted to become the ultimate life-form by hacking off alien limbs and ripping out their organs to graft to himself. He's basically a serial killer with all sorts of freaky alien powers... scary in itself, before you see what he really looks like...
- In his very first appearance he manages to push Kay's buttons expertly enough to provoke the normally calm and collected agent into going solo against him. He is that good at manipulation.
- Also, said confrontation has Kay preparing for a Mutual Kill by using a poison gas that Alpha's alien hostage can survive - a poison gas that can melt human lungs. He is one second away from pulling the trigger and dooming himself to die with his nemesis when Jay and Elle show up. Probably the closest Kay came to death in the series.
- Even worse, he's a recurring villain, and a big contender for the series' Big Bad. So of course, he is still running around harvesting organs. Each subsequent appearance he becomes more and more inhuman in appearance, until he looks absolutely nothing like he did in his first appearance, with the only thing left of him being his brain.
- Piggybacking on that, Alpha first starts as looking human enough that he can wear a MIB suit, though he exposes himself as having several alien heads attached to his own body. Then he appears shrivelled, balding and old. He then evolves, gaining a cybernetic eye and becoming a hunched being with nothing human EXCEPT his head. Eventually, after a jaunt in the Antarctic where our heroes knock him into the freezing waters, he emerges with his body entirely black from frostbite, pieces crumbling away and his lips and nose gone, with his face almost skull-like as he approaches, killing and absorbing a normal human.
- There's also the fact of Alpha having once been Agent K's partner and mentor. Kay trusted him as a dear friend, before Alpha eventually betrayed the Men in Black and even his own species (he was not only turning himself into a literal monster, but also secretly collaborating with Vangus and the Ixions for a cancelled invasion of Earth). It's no wonder why Kay is so jaded and reserved most of the time.
- Vangus, the co-antagonist of the two-part "The Endgame Syndrome", can easily match Alpha in terms of vileness (if not even more so). Vangus is an Ixion commander who leads an invasion of Earth in order to steal all oil from the planet. When the Earthlings successfully counter-attack with the help of some alien allies, he decides to launch a missile that would kill everyone on the planet while saving the petroleum for himself, effectively screwing over Alpha (who intended to enslave any surviving humans). Although his evil plans are fortunately thwarted, Vangus escapes unharmed in the end.
- Quick Clones. They are every bit as intelligent and self-aware as the person they were cloned from, but are treated as completely expendable. They melt into goo after a few hours at most and they have a conveniently-placed Self-Destruct Button that can be used to terminate them at any time. Before they expire they start speaking gibberish, implying that their mind is rapidly deteriorating.
- Some of the uses are justified - a decoy with a bomb or a mission critical option - but it's shown that Elle at least regularly uses them to deal with the workload.
- The danger of using quick clones is also shown, especially for field agents like Jay. In "The Quick Clone Syndrome" Jay is fed up of his workload and convinces Elle to send his clone out with Kay. This goes reasonably well - till, in the midst of a confrontation with Alpha, the clone (who was holding Alpha at gunpoint) melts down. Kay was probably very lucky that Alpha simply used the opportunity to flee instead of attacking - that would have meant Kay was done for, since he had already been disarmed.
- Jeebs is usually a Butt-Monkey who is constantly switches sides. The Heads You Lose Syndrome shows that not even children are safe from Jeebs’ Dirty Coward behavior. To avoid repercussions from Alpha, he abducts an alien baby in front of his parents so Alpha can cut off the child’s arm. The dark element is lightened by the fact that the baby quickly pummels him not too long after. This is truly Jeebs’ darkest and lowest moment in the series to the point you don’t feel that bad for him when he crashes into Mount Rushmore at the end of the episode.
