Zed hires a new alien field agent, infuriating Elle who's been bucking for a promotion to the field for months. She proposes a replacement for herself in the lab; Dr. Zeeltor, a wacky eccentric genius, whom Zed knows by reputation. Zed agrees to give it a try and promotes Elle, but she's mortified to discover her new partner is Agent X. Meanwhile, Jay is having minor aches and pains, thinking nothing of it not realizing he's got a life threatening neuro-spinal disorder resulting from exposure to a thistly alien called a Bovus. He refuses to let the new Dr. Zeeltor ...

Kay and Jay go on a Worm-rescue mission to the distant, Roman-esque planet of Empiria. The WORMS have been abducted from the MiB coffee room in the mistaken belief that they are the legendary warriors, the WORPS...and now have to fight in the Coliseum for the entertainment of the hard-to-please emperor. The rescue doesn't go all that smoothly; Kay gets swallowed by an arena beast and Jay is forced to face off with the Worms in a battle to the death. And just when things couldn't get any hairier, the actual Worps show up, angry about the Worms stealing their thunder ...

After a coup attempt fails on the distant planet of Naar, its Emperor fears that rebels will try to kidnap his son Raax, who's on Earth disguised as a high school student. He asks MiB for help. With a special weapon pen and a backpack provided by Zeeltor, Jay goes undercover. Alas, he runs afoul of the Principal, incurs the wrath of two Jocks, (who may be the kidnappers in disguise) and with the unwanted "help" of the Worms who end up blowing his cover. Kay eventually shows up to bust Jay's chops as a substitute teacher. Things come to a head when a Worm prank ...

KAY and ZED of a case from the early days of MIB. Former MIB chief ALPHA was in charge of the investigation, but encrypted the data files. At JAY's suggestion the MIBs visit Alpha in the maximum security detention block, where he's in a pod, being kept alive by machinery. Jay sneaks back into the secured area to see Alpha again. As Alpha challenges Jay to a chess game, Jay coaxes out info, but who's finessing whom in this highly charged cat and mouse game? Jay smugly passes off Alpha's info as his own research, based on his keen "instincts" informing the MiBs that ...

The pursuit of an illegal alien time jumper leads Kay and Jay to Jeebs' shop where the Worm Guys happen to be in mid-transaction. When Kay and Jay try to arrest the perp, a battle ensues, during which the Worm Guys are accidentally slimed with a mysterious substance. The alien perp then uses his Quarthanite Time Jumper to open a time portal to escape. Jay overzealously pursues and finds himself inadvertently sucked into the portal as well, winding up in a disturbing future where Worm Guys rule the Earth. Kay eventually follows Jay into the future, hooking up with an ...

The FMECKS, seeking a new home, have stolen a micro-planet, Thahzia, but KAY takes it back from them in a struggle that leaves JAY temporarily turned to stone! While Zeeltor tries to cure Jay, Kay is shrunk down and sent into the SMALL ORB containing the planet to help calm the locals and provide temporary climatic relief. But when the Fmecks return to MiB for the orb, it gets loose and ends up being used by the oblivious Worms in a sandlot baseball game. Jay takes a turn at bat and knocks the orb (not knowing what it is) into the city. When Jay finds out the horrible...

After Jay accidentally eats an alien hot sauce at an MiB reception for the formerly war-like, now supposedly peace-loving Hoon'Taak Federation he develops human torch-like fire powers. At first Jay is appalled and embarrassed by his combustible condition, but after he uses his fire powers to save Kay's life and bust an alien smuggling ring, he becomes cocky about his new abilities. But then, Zeeltor discovers that by using his fire powers Jay's gradually destroying his internal organs any further use could prove fatal. Meanwhile, MiB discovers that HQ has been taken ...

An alien who hid from an alien gang in a circus seeks help from MiB when the gang returns to capture him.

After Jay scores a less-than-stellar "67" out of 100 in Zeeltor's VBE (Virtual Battlefield Environment) he gets endlessly ribbed by fellow agents. Eager to redeem himself in the field Jay volunteers to guard a visiting Dignitary. Unfortunately, the assignment ends up in more humiliation for Jay; the Dignitary is just not comfortable being guarded by an agent who scored a mere 67. Jay sneaks back into the VBE late at night, but what he doesn't know is that, at Zed's request, Zeeltor has retooled the VBE. It now contains more dangerous nemeses and opponents. Worse, due ...

Drekk escapes from alien prison and comes to Earth seeking revenge. Same time an alien TV crew filming MIB agents at work.

An alien calling himself Cosmosis acts like super hero and defends the city from evil. At same time MIB fights with sparky alien and Jay pretends to be as Swiss Army Man evil hero to catch Cosmosis.

Alpha is back and with Vangus and the Ixions they are targeting the Earth. Because of alien invasion Zed reveals MIB's and aliens existence to the president and all world. [Continued.]

When Earth is under attack, other races come to help against the invasion. The Ixions plan to use a planet killer weapon against the Earth. This is the final battle for humanity.