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.

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.

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.

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.

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.

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.

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.

It's Halloween night and trick-or-treating with the worms gets dangerous when Jay comes across an alien that kidnaps children.

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.

Jay and Kay have to stop alien terrorist Quintoon's plans to raise the legendary Atlantis continent.

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.

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 and Kay have to contend with a recently awakened Hyperian, which is dressed like an ancient Egyptian Mummy.

During pursuit of a large criminal Worm, Jay gets sent to the future and finds that the Worms rule all of Earth.

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.

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.

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.

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

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.

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.