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.
The Fmeks are stealing human suits from their enemies, the Arquillians. Jay gets shrunk down to their tiny size to find out what the Fmeks are up to.
Jay gets Elle to make him a set of quick clones so he can catch up on some much needed sleep. But while Jay snoozes, Alpha resurfaces and uses one of the quick clones to capture Zed.
Alpha is back and his alien attachments are falling apart. At first, he forces Jeebs to locate new alien body parts for him. But when Alpha discovers Troy the symbiote is at MIB, his plans change.
Drekk, an old friend of Frank the Pug, is running loose on Earth. And Frank faces getting boiled alive if he helps Jay and Kay apprehend him.
The Queen Bug puts out a bounty on the MIB agent that took out dearly departed Edgar. Now Elle is running from some nasty bugs looking to collect the reward.
It's Halloween night and trick-or-treating with the worms gets dangerous when Jay comes across an alien that kidnaps children.
A sonic powered alien named Aldoosi escapes from Eileen and her new partner, Eidi. To track this fugitive down, Kay works with Eileen and Jay works with Eidi.
Parasites spread by alien seeds take over MIB and threaten the world. As the remaining agents try to stop it, Jay can't keep his mouth shut since he's accidentally been given a truth serum.
Preparing to conquer Earth, the Fmeks break into MIB to get their tiny hands on a growth forumla. They mistake one of the worms to be able to make the formula and capture him.
It's up to MIB to save Christmas when Drekk kidnaps Santa Claus.
The Tomassitron Matter Amplifier grants Jay, Kay and Elle super powers as well as three alien criminals, leading to a super showdown.
Jay and Kay head to Hollywood to investigate the disappearances of alien actors.
Alpha and Dak, Jeeb's brother, take over MIB's Blackguard satellite. Jay and Kay blast into space to stop them before they destroy MIB with it.
Two Kalifadik law enforcement officials begin punishing the guilty on Earth, using teleportation guns to send them to an alien prison. As MIB tries to stop them, Jay and one of the worms pass through each in mid-teleportation and slowly turn into each other.
Merged together, Alpha and Dak find themselves in Antartica where a powerful alien spaceship lies buried.
Frank the Pug meets an alien named Veronica and falls in love. But what he doesn't know is that Veronica works for Javkor, who is out to steal MIB's most powerful weapons.
Jay and Kay have to stop alien terrorist Quintoon's plans to raise the legendary Atlantis continent.
When MIB fails to stop a Metaphite that threatens Phoenix, Jay and Kay have to travel back in time to the wild west to find the Metaphite's then vulnerable cocoon.
The Bug Queen herself has come to Earth and is hiding in hotel, waiting for her eggs to be able to take over. Making things worse for MIB is the presence of the Emperor Worm, who happens to be staying in the exact same hotel as the Bugs.
When Zed orders the worms to be sent back to their home after another mishap, Jay does whatever he can to prove their innocence.
Kay is blinded by a Darkon ray and will need Jay's help to stop the Darkons from creating a permanent eclipse.
Zed surprises everyone when he decides it's time to retire. Jay gets partnered with Elle since Kay is chosen to be the new head of MIB. As Zed is neuralized and embarks on a life of fishing in Long Island, Alpha returns more powerful than ever.
Jay accidentally swallows an alien egg and becomes pregnant. Meanwhile, the Fmeks are shrinking everything in sight.
Jay and Kay have to contend with a recently awakened Hyperian, which is dressed like an ancient Egyptian Mummy.
The Stellairian leader comes to Earth for peace talks and Jay and Kay have to watch over his daughter, Kima. When she is kidnapped by Frostifarians, her age regressing hypo-spray breaks loose. Now as Kima grows older, Kay begins turning into a baby.
Jay and Kay are moving fast to stop the take over of Earth by the Tunstons, whose king is hiding out in Frank the Pug's body.
Jay's destructive joyride in the LTD causes him to be thrown out of MIB. Now, Jay is neuralized and back in the NYPD just as the Bugs arrive.
Changes abound at MIB as Dr. Zeeltor takes over in the lab for Elle, who has become a field agent and gotten partnered with an alien named Agent X. As these new changes set in, MIB has to stop New York from being devoured by a Barooga.
Jay and Kay have to rescue the worms from an alien world similar to Ancient Rome.
Jay poses as a high school student to protect an alien prince from alien terrorists.
Thirty years ago, an Ixion named Vangus came to Earth and was stopped by an MIB agent. Now when Vangus returns, MIB seeks answers from the agent that stopped him: Alpha.
During pursuit of a large criminal Worm, Jay gets sent to the future and finds that the Worms rule all of Earth.
The Fmeks are back and trying to take over a tiny planet that resembles a baseball. To make matters worse, Kay is on the tiny planet and things are getting very hot.
After eating some alien food, Jay gains the ability to throw fire. But this new power will have serious consequences if he keeps using it.
A member of a witness protection program for aliens is on the run from an intergalatic gang called The Association when they discover he's on Earth.
Jay gets a low score on MIB's new virtual reality training test and the embarassment eventually forces him to try again. But this time the game goes haywire and the dangers Jay faces become deadly.
An alien tv crew comes to Earth to film MIB agents on the job just as Drekk returns to cause trouble.
A super hero caling himself Cosmosis emerges to defend the city from evil, but he's really an alien looking to put his powers to good use. However, MIB feels his new profession could attract trouble for Earth, so they try to lure him out using Jay as bait.
Alpha, Vangus and the Ixions return to Earth, working together to threaten all life on the planet. With invasion imminent, Zed decides to reveal MIB's existence to the world.
With MIB having success in coordinating resistance against the invasion, the Ixions plan to unleash a weapon that will kill everyone on Earth. Jay and Kay will fight Alpha in the final battle for humanity.
