Tired of long days, Jay uses quick clones, temporary doubles that melt down after a few hours, to do his job while he sleeps. When the evil Alpha gets hold of a melted-down Jay Clone, he uses the DNA to create a quick clone of his own: Jay's evil twin.
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Tiny extra-terrestrial terrorists (called Fmecks) are stealing the high-tech human-suits that allow Arquillians to disguise themselves on Earth. Jay is shrunk down the Arquillian size to catch the thieves, and uncovers a plot to destroy the Arquillian home world.
Troy the Symbiote returns to the MIB. But he is kidnapped by the evil Alpha, and forced to serve in Alpha's menagerie of alien organs. With symbiote powers, Alpha will be unstoppable. The Men in Black have less than 20 hours to separate Troy from Alpha, or the meld becomes permanent!
Drekk, an alien criminal, flees to Earth after escaping from an Intergalactic Prison. Kay and Jay find out that Frank the pug knows Drekk and they talk Frank into helping them capture the criminal. When Drekk finds out that Frank ratted him out, he busts out and returns to Earth for revenge.
Three bugs, Edwin, Dung, and Moe, seek revenge against the MIB agent who killed Edgar. Since it was Elle who pulled the trigger, she's the one in danger!
Suspicions of the supernatural abound when a Barthok slave trader is mistaken for an evil spirit, because of his pumpkin-shaped head. When the slave trader makes off with one of the worm guys, it's up to the MIB to get him back. Meanwhile at MIB HQ, a Napieran energy being is mistaken for a poltergeist. The result: Hundreds of scared aliens flee headquarters in fear and flood into the streets of New York.
Aileen, the alien cop, returns to Earth, accompanied by her new partner, Edie. They are transporting Auduzi, an alien criminal who uses his voice as a weapon. When Auduzi escapes, Kay and Jay team up with the alien cops to catch him.
An alien smuggler brings some strange seeds to Earth. When the MIB bust the smuggler, the seeds sprout legs and escape. Although they can't germinate on Earth, a quick trip through Frank the pug's stomach produces the necessary soil conditions. The seeds hatch out and reveal themselves to be the Nrak, an intelligent species of plant. In true "Bodysnatchers" fashion, the Nrak put down roots and begin enslaving the human race.
The Fmecks are back! This time they've set their sights on taking over Earth. Just one problem: They'll need to get a hold of a super-secret growth formula, so they can "open doors and reach things" once they've taken over. Their attempt to kidnap the scientist who invented the growth formula goes awry when they accidentally kidnap a worm guy.
While investigating an attempted robbery, Kay, Jay, and Elle are exposed to an alien device that gives them super powers. Since the alien criminals who attempted the robbery were also exposed, the MIB agents must use their newfound abilities to defeat these super-villains.
It turns out that all those aliens we see in the movies are real aliens. When alien actors keep disappearing, Kay and Jay are sent to Hollywood to investigate. While solving the mystery, the MIB come face to face with every Hollywood stereotype imaginable, and some that are beyond imagination!
Santa is missing, kidnapped by Drekk. Santa's elves come to MIB for help. If Kay and Jay can't free Santa before midnight, Zed will have to take Santa's place, delivering toys to children all over the world.
Elle is overseeing the startup of MIB's own space station, the Blackguard 1. Alien mercenaries, led by Dack, take over the station. Their boss, Alpha, intends to use the station's solar cannon to destroy MIB. Elle sabotages the weapon, buying enough time for Kay and Jay to head into space. The question is: Can the MIB take back the station before Alpha gets the cannon working again?