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.
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.
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.
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.
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.
