J makes himself a target of the Skraaldians when during a mission to stop one of their kind multiplying in the sewers, he accidentally destroys it rather than freeze it when it attacks K. Learning he is not safe because they can disguise themselves easily, have a hive mentality, and can lock onto his DNA, K is forced to find a solution to save his partner, before J is put into the "soup".

A crash landing in the woods leads to K and J encountering Treblor, an alien cop seeking a fugitive named Z-Ron, the downed ship's occupant. But nothing is what it seems for the two MIB agents, when they discover certain facts about their two new arrivals.

When a Charnock lands on Earth and aggressively attempts to take a Void Density Core from Jeebs's shop, K and J quickly discover that Frank had been there and accidentally swallowed it. Now the pair find themselves seeking to protect him, whilst trying to get it out and deactivate it before it can start sucking everything into itself, including New York City.

K discovers that the theft of a Sintillian heart was the work of Alpha, his former mentor and MIB agent, who stole a Cosmic Integrator to make himself stronger. While K is eager to go it alone, J refuse to let his partner do so, and so is in a race against time to find out where he and Alpha are.

When Dirndl, a Tarkan Trade Minister from Tarka, arrives on Earth for an alien conference, J accidentally incapacitates his Tarkan bodyguard. Z quickly assign him to work undercover as his replacement during the conference, in order to route out an assassin seeking to eliminate him, but with so many aliens attending, it's a tall order for the MIB agent.

J has always wanted to know more about K, and gets more than he bargained for when he accidentally neuralyzes him back to when K was sixteen years old. While J finds himself trying to get K to return to MIB HQ, matters are complicated when a group of Chop-Shoppers, black market starship thieves, kidnap him, leading J to call for help from L.

J offers to replace K for an assignment, when a microbe alien species, the Millicrons, unintentionally infect his partner. His assignment turns out to the safe transportation of a teenage symbiote named Troy, who needs to be brought back to New York City within twenty hours before he absords J, but matters are complicated when Buzzard is hired by a mysterious employer to grab the symbiote.

MIB finds themselves dealing with an alien called an Inanimate - a shapeshifter capable of disguising itself as inanimate objects. To assist the organisation, an intergalactic cop named Eileen arrives, and is soon partnered with K, leaving J jealous and eager to keep a close eye on him, despite being partnered with U.

After a human is drained of their bodily fluids, K and J discover it to be the work of an Alcidian named Forbus. They quickly discover that he is both mentally unstable and targeting anyone who films or photographs him, but matters are complicated when Forbus creates a mental link with K that causes him to experience anything the Alcidian does, and is slowly making him as unbalanced as he is.

J suddenly becomes the smartest man on the planet when he mistakes a Cerebro-Accelerator for a pair of head phones. But the new intelligence comes at a price - in twenty-two hours, his brain will explode. Matters are not helped when an alien-hating bigot uses a time travel device to begin erasing the five founders of MIB from existence, leaving J the only person to stop him.

Investigations into the sudden coma states of the crew of a returning NASA space shuttle leads to K, J and L uncovering it as the work of the Vermax, an alien species that feeds on the chemicals formed from dreams. When bringing down more Vermax at the shuttle's landing site, J prevents L being the latest target of one and is soon put into a deep sleep. To save him by getting him to wake up, L risks her life with restricted technology in order to enter his dreams, despite the Vermax doing everything to stop her.

MIB finds itself attempting to stop an alien race known as the Blastula from increasing Earth's temperature as part of a plot to colonize the planet, but J has suspicions that his partner K is acting odd, and that he might be working for them.

A break-out in MIB's prison ward incapacitates most of the building and leaves Z and K as prisoners of the mastermind - Dr. Lupo. Because J and the Worms were sealed in a vault getting coffee and thus not put out of action, they become the only ones capable of rescuing Z and K and stopping the breakout of Lupo and two equally dangerous criminal inmates who caused the Prison riot.

A spate of human suit thefts and the abduction of their owners, the Arquillians, is uncovered to be the work of their enemies, the Fmeks. To learn what they are planning, MIB shrinks J to their size and tasks him and K to investigate. It soon becomes clear that the thefts are part of a much bigger plan.

Working long hours finally becomes too much for J, so when he discovers that L is using a quick clone to help her get rest, he quickly jumps at the chance of doing the same. But matters become complicated when Alpha uses the remains of one of his quick clones to create a J-lookalike, in order to kidnap Z's brain for information he needs.

With his alien attachments slowly falling apart, Alpha coerces Jeebs to steal new parts. That is, until he learns that Troy the symbiote is at MIB on an internship, and decides to go after him. K, L and J soon find themselves attempting to stop this, with the help of Troy's mother.

Frank's former cellmate, Drekk, an alien who can generate flames and intense heat from his hands, has escaped and is on the loose on Earth. MIB quickly finds itself trying to locate and capture him through Frank, but when Drekk escapes, he forces Frank to lead K and J into a trap.

MIB learns that a bounty has been placed on L by the Queen of the Bugs, for her part in Edgar's demise. With several bugs, including Edgar's own brother Edwin, arriving on Earth to claim it, and L out in the field, K and J find themselves racing to find and protect her before one the bugs carts her off the planet. Meanwhile J gets roped into the worms scheme of showing their Emperor that they're big shot MIB agents.

J finds himself escorting the Worms as they head out trick-or-treating on Halloween night, only to discover, along with K and U, that there's an alien who just arrived, who seeks to kidnap children for slavery. Meanwhile, MIB's Headquarters suddenly experiences a power cut and weird things slowly begin happening, leading to Z and L trying to find a scientific reason for the situation.

Eileen returns to Earth, refuelling her ship alongside her new partner, Eidi, while they are transporting a sonic-powered alien fugitive named Aldoosi. But when he escapes, MIB coordinates a joint operation to capture him before he can leave the planet. While K is partnered with Eileen, J finds himself working Eidi and discovers that the two are quite similar.

Contraband goods that recently arrived turn out to be an alien parasitic species that spreads through the use of seeder plants and spores. With much of MIB incapacitated and the world threatened, K and L find themselves seeking the species' nucleus in order to inject it with an antibody, though the matter is not helped by J, who is accidentally given a truth serum and cannot keep quiet.

Seeking revenge for the loss of their world, the Fmeks attempt to get a growth formula by capturing the alien scientist that created it while they are at MIB. A group of Fmeks assigned to this task mistakenly believe one of the Worms is their target and capture them. When one of the group is left behind and discovers their error, L finds herself a prisoner upon walking in on them after they use the growth serum on themselves.

Christmas is on hold at MIB as K and J find themselves on the hunt for Santa Claus, soon after Drekk and a group of alien yetis kidnap him from his workshop and steal all of the toys his "elves" were working on. Aided by one of Santa's elves, the pair soon discover that Drekk's employers are not what were expected.

An alien ship in Earth's orbit is breached by three alien criminal seeking to steal a Tomassitron Matter Amplifier. Although the device is activated in the attempted theft, MIB prevents it being stolen by bringing the ship to Earth. While K, J and L deactivate the Amplifier, all three discover that they have gained super powers from the device's rays, and quickly find themselves the only ones who can stop the criminals when they too also develop powers of their own.

A spate of alien actor abductions in Hollywood leads to K and J meeting with MIB's "Agency" division in Los Angeles to uncover the culprit behind the crime. While J believes the suspect is a former alien actor, K reviews the films of the missing actors to uncover the truth behind their disappearances.

Alpha returns, and with the aid of Jeebs' brother Dax takes control of MIB's new Blackguard satellite weapon system, which can destroy incoming asteroids or specific targets on Earth. When MIB learns that L thwarted their initial attempt to destroy the organization, and that Jeebs has been contacted for a replacement part to repair the weapon system, K and J are assigned to head out into outer space and stop Alpha before he can get another chance to fire the weapon.

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, J and one of the Worms pass through each in mid-teleportation and slowly turn into each other.

Merged, Alpha and Dak find themselves in Antarctica where a powerful alien spaceship lies buried. It is up to K, J, Jeebs and the Worms to stop them from using it.

Frank the Pug meets an alien named Veronica and falls in love. But what he does not know is that Veronica works for Javkor, who is out to steal MIB's most powerful weapons.

K and J team up with the ocean patrolling MIB operative Agent C when alien terrorist Quintoon's plans to raise the legendary Atlantis continent. However K and J quickly learn that the isolation has made C go mad.

When MIB fails to stop a Metaphite that threatens Phoenix, J and K have to travel back in time to the Wild West to find the Metaphite's then vulnerable cocoon. Unfortunately, a Vexron living in that time is determined to make sure that they do not succeed.

The Bug Queen herself has come to Earth and is hiding in a hotel, waiting for her eggs to hatch and take over. Making things more difficult for MIB is the presence of the Emperor Worm, who happens to be staying in the exact same hotel as the Bugs.

When Z orders the Worms to be sent back to their home planet after another mishap, J does whatever he can to prove their innocence.

K is blinded by a Darkon ray and will need J's help to stop the Darkons from creating a permanent eclipse.

Z surprises everyone when he decides it is time to retire. J gets partnered with L since K is chosen to be the new head of MIB. As Z is neuralyzed and embarks on a life of fishing in Long Island, Alpha returns more powerful than ever.

J accidentally swallows an alien egg and becomes pregnant. Meanwhile, the Fmeks are shrinking everything in sight.

K and J have to contend with a recently awakened Hyperian, which is dressed like an ancient Egyptian mummy. Now the MIB have to stop it from getting off world or risk an invasion.

The Stellairian leader comes to Earth for peace talks and K and J 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, K begins turning into a baby.

K and J are moving fast to stop the take over of Earth by the Tunstons, whose king is hiding out in Frank the Pug's body.

After J goes for a joyride using the LTD, he ends up getting terminated from the MIB. He is then neuralyzed and sent back to the NYPD. However, the MIB need him back when they discover not only has the Bug Queen resurfaced, but J found out their base of operations while out for a spin.

Changes abound at MIB as Dr. Zeeltor takes over in the lab from L, 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.

K and J have to rescue the Worms from an alien world similar to Ancient Rome.

J 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, K is on the tiny planet and things are getting very hot.

After eating some alien food, J 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 intergalactic gang called The Association when they discover he is on Earth. J's lead on The Association leads him to an alien circus, which brings back terrible memories of a clown that terrified him when he was a child.

J gets a low score on MIB's new virtual reality training test and the embarrassment eventually forces him to try again. But this time the game goes haywire and the dangers J 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 calling himself Cosmosis emerges to defend the city from evil, but he is 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 J 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. K and J will fight Alpha and Vangus in the final battle for humanity.