In MIB 2, J mentions he'd defeated an alien invasion while K's memory was gone; obviously it was the one in Independence Day. When the aliens invaded, the MIB slipped several of its agents into the military as covert operatives. Agent J swapped out Jeff Goldblum's Macbook with an advanced MIB computer capable of hacking the aliens, and also switched the human atomic bomb with a more powerful explosive. Once the rubble had been rebuilt, the MIB used a massive neuralizer burst to make everyone forget..