Two Kalifadik law enforcement officials begin to send aliens to an prison with teleportation guns. MIB tries to stop them, but Jay and one of the worms pass through each in teleportation and turn into each other.

When an escape pod from a Russian space station jettisons away and eventually crash lands in the Antarctic, Kay and Jay head south, way south, to investigate. Unbeknownst to them, the worm guys have stowed away, thinking they are headed to South America, home of the coffee bean. What Kay and Jay discover is that Alpha was in the pod, his body having merged with Dack, Jeebs' obnoxious brother, while Apha and Dack were floating in space. With the help of Jeebs who arrives in his pod, Dack and Alpha unearth a "Bioship" long buried beneath the Antarctic ice. If Alpha/Dack...

Frank meets an alien named Veronica and starts dating with her. But Veronica works for Javkor, who wants to steal MIB's most powerful weapons.

Jay and Kay are summoned to a remote MIB submarine outpost manned by the cabin-fevered Agent C, in order to stop intergalactic terrorist/zealot Quin'toon, who has taken alien hostages and plans to raise the ancient, long-abandoned, alien-built continent of Atlantis from the ocean floor. As Zed points out, this would not only blow MIB's "cover-up of aliens' existence", but worse, cause tidal waves of such force as to wipe out half the East Coast. During the mission, Jay is inoculated with an amphibious serum to allow him to survive the perilous depths, but is revolted ...

When a rampaging alien called a Metaphite breaks out of its cocoon and threatens Phoenix, MiB is called in to stop it. Unfortunately, all efforts prove useless against the giant alien that is basically a living nuclear reactor. The only solution is to use a "Time Jumper' to travel back one hundred and thirty years in the past when the Metaphite cocoon is vulnerable. Upon arriving smack dab in the middle of the wild west, Kay and Jay locate the cocoon only to be ambushed by another alien, a Vexron, which grabs the Metaphite cocoon and escapes. Kay and Jay (soon joined ...

A Bug Queen is in town with her two bug escorts and it is up to MiB to find her before she can lay her eggs and infest the city. To make matters more complicated, the Emperor Worm is also in town, mutilating his English and basically making life tough on the Worm Guys. The Emperor Worm insists on being put up in a hotel worthy of his stature which, unfortunately, turns out to be the same one which the Bug Queen has chosen for her lair. The Emperor is taken hostage and it's up to Kay, Jay, and Elle (along with some unsolicited help from the Worms Guys who are trying to...

When the Worm Guys apparently are responsible for a near nuclear meltdown at MiB, Zed orders them deported. But Jay comes across evidence that suggests that the Worm Guys were merely in the wrong place at the wrong time and that the meltdown was an act of sabotage. To prove his theory, Jay must put his MiB career on the line by disobeying orders and replacing the Worm Guys with quick clones before their transport ship blasts off. Together with the Worm Guys, Jay pieces together the mystery and discovers that the real perp is an unassuming MiB janitor named Zelgar who ...

Kay is blinded by a Darkons ray gun and needs Jay's help to stop the Darkons on the Moon from creating a permanent eclipse.

Zed makes a stunning announcement: He's retiring; he's decided he's too old and weary to lead MiB into the next century. Kay will be his replacement; Jay will get a new partner. Zed is given a retirement party, neuralized and immediately "re-located" to pursue a new life fishing on Long Island. But it seems Zed's timing couldn't be worse: Alpha is back, is up to something big and must be stopped. With Kay promoted to chief, Jay is eager to get himself a new junior partner he can boss around. But his bubble is burst when he's assigned a new partner - Elle. Out in the ...

Jay accidentally swallows an alien egg and becomes pregnant. Fmeks are back and shrinking landmarks in New York.

Kay and Jay are called in to investigate when a 5,000-year-old Mummy comes to life, ransacks a museum and escapes. They bring with them an unlikely expert in Egyptology...Frank The Pug. The MiB agents and Frank soon determine that the Mummy is actually an ancient alien scout sent by a war-hungry race called the Hyperians. Just as Kay, Jay and Frank are about to thwart the rampaging Hyperian Mummy, Jeebs whisks the alien back to Egypt in his transport pod. Our trio follows, with Frank withholding the fact he and Jeebs are both actually after the powerful "Scepter of ...

The new leader of a terrorist race of aliens called Stellairians wants to embark on a new era of peace and comes to Earth for negotiations ... bringing along his spoiled teenage daughter. The Stellairians age rapidly in Earth's atmosphere - about 100 years in a day - so Kima is reminded to take her hypo-spray, located on a chain around her neck. Kay and Jay are assigned baby-sitting duty, and take Kima to the mall - where a group of Frostifarian Kidnappers (who had their icy planet scorched by Skon) create a diversion and nab Kima. During the chase, her hypo-spray ...

Kay AND Jay track an unregistered, unidentified alien arrival, who turns out to be the King of a slug-like race called Tunstons. These robosuited aliens are plotting to take over New York City, and then the world, by covering ft in the bacterial ooze that Tunstons need to survive. Unfortunately, the giant robosuit created for the KING is damaged in a battle with Kay and Jay, so the alien King must take up temporary residence in Frank the Pug. As most everyone in the city gets sick from the bacterial ooze, the Tunston King plots to seed the clouds and trigger a ...

After one maverick incident too many, Agent J is expelled from MiB and has his memories erased - most of them, as a recurring vision of the bugs gets him back.