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.
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. Unfortunately, a Vexron living in that time is determined to make sure that they don't succeed.
The Bug Queen herself has come to Earth and is hiding in hotel, waiting for her eggs to be able 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.
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 neuralyzed 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.