Agents J and K are back...in time. J has seen some inexplicable things in his 15 years with the Men in Black, but nothing, not even aliens, perplexes him as much as his wry, reticent partner. But when K's life and the fate of the planet are put at stake, Agent J will have to travel back in time to put things right. J discovers that there are secrets to the universe that K never told him - secrets that will reveal themselves as he teams up with the young Agent K to save his partner, the agency, and the future of humankind.

A group of scientists in San Francisco struggle to stay alive in the aftermath of a plague that is wiping out humanity, while Caesar tries to maintain dominance over his community of intelligent apes.