Season 1

While trying to get Skraaldians out of New York sewers, Jay uses his Noisy Cricket on one and kills it. Problem is, all Skraaldians are psychically linked and know what Jay did. And every last one will go after him to settle the score.

Jay and Kay investigate a crashed alien ship in the woods when they encounter Treblor, an alien cop from the Zombarian Retrieval Department. Treblor says the owner of the crashed ship is a fugitive named Z-Ron. While Jay goes out ahead to get Z-Ron, Kay learns Treblor isn't who he says he is.

A Charnok has to come to Earth and ransacked Jeebs' pawn shop as well as hunting reliable MIB informant, Frank the Pug. After some investigating, Jay and Kay learn the Charnok was trying to buy a Void Density Core from Jeebs, who didn't want to sell it. Frank made off with it during the fight and accidentally swallowed it. Now the MIB have to get the VDC out of him before it detonates and sucks the city into a miniature black hole.

Investigating the theft of a Sintillian heart, Kay learns the culprit is Alpha, his former mentor and the man who left him for dead years ago. But Jay and Kay discover Alpha now has multiple body parts grafted onto his body, becoming even more dangerous.

Jay goes undercover as a Tarkan bodyguard at an alien conference to protect Dirndl, Trade Minister of Tarka, from an alien assassin.

While trying to stop alien thieves known as Chop Shoppers, Jay's accidental use of the Neuralizer erases Kay's memories and makes him think he is sixteen.

When Kay is infected with Millicrons, Jay takes his place on an assignment to transport a symbiote named Troy to New York City. He has to do it within twenty hours or be permanently absorbed by Troy. But Buzzard returns and is looking to capture the symbiote for his mysterious boss.

An Inanimate, a shapeshifter capable of disgusing itself as inanimate objects, escapes from prison to Earth. But the MIB get some help from Eileen, an intergalactic cop that stirs up some old feelings for Kay.

An insane Alcidian named Forbus is hunting humans, draining them of their bodily fluids. But during the pursuit, Forbus forms a psychic link with Kay, making him feel whatever he feels.

Jay mistakes a Cerebro-Accelerator for a pair of head phones, making him the smartest man on Earth. However, this will also cause his brain to explode in twenty-two hours. But his advanced brain is MIB's only hope when someone uses time travel to erase the five founders of MIB from existence.

Alien dream eaters known as the Vermax attack the crew of a returning NASA space shuttle. When Jay, Kay and Elle arrive at the landing sight, a Vermax attaches itself to Jay and sends him into a deep sleep. Elle enters Jay's dreams to get him to wake up and remove the Vermax.

The Blastula are increasing the temperature on Earth in their plot to colonize the planet.

Dr. Lupo and other inmates of MIB's prison ward manage to break out and incapacitate most of MIB. Only Jay and the worms can save the day.