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.
- 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."
- 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. His spaceship is filled with about a dozen different alien skeletons, and decides 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.
- 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...
- 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 destroy 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.