Jay and Kay are summoned to a remote MIB submarine outpost manned by the cabin-fevered Agent C, in order to stop intergalactic terrorist/zealot Quin'toon, who has taken alien hostages and plans to raise the ancient, long-abandoned, alien-built continent of Atlantis from the ocean floor. As Zed points out, this would not only blow MIB's "cover-up of aliens' existence", but worse, cause tidal waves of such force as to wipe out half the East Coast. During the mission, Jay is inoculated with an amphibious serum to allow him to survive the perilous depths, but is revolted to discover that its also given him gills and webbed fingers. Jay and Kay manage to overcome Quin'toon and his Robot minions and stop the Atlantis raising machinery at the last moment. But not fast enough: a killer wave is heading for a populated tropical island and our MiB duo are the only ones who can stop it.