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.
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.
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.
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.
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.
