What's Up With the Ending?
Men in Black caps its story with a classic sci-fi adventure ending: the evil alien Bug goes boom, the good guys save the world from annihilation, and they rescue the damsel from a terrible fate. To be fair, Laurel actually rescues herself and then saves Jay and Kay from being eaten by the bug's upper half. But neither agent is so obsessed with machismo to have a problem with this tweak to the formula.
Most science fiction films might decide this is a fine place to roll the credits, but while this classic ending concludes the story, it doesn't wrap up the development of its characters. For that, Men in Black has one more plot twist before it bows out.
Passing the Torch
After stopping at an all-night dry cleaner to have the bug guts scrubbed from their suits, Kay and Jay arrive at the front of MiB headquarters. Jay asks Kay not to erase Laurel's memories since she did help them bust the Bug. Kay takes out the neuralyzer anyway but reveals it isn't for her. It's for him. He's been training Jay to be his replacement all along.
JAY: Kay…
KAY: I've just been down the gullet of an interstellar cockroach. That's one of a hundred memories that I don't want. (Jay puts on his glasses.)
KAY: See you around, Jay.
JAY: No, you won't.
We should notice two things about this scene. First, the Men in Black have an awful retirement plan. Second, Kay's send off mirrors the opening scene with Dee. Like Dee, Kay knows his time as an agent has come to an end and is willing to let go gracefully. Unlike Dee, Kay isn't too fond of the chase and is grateful to unload the emotional burdens he's been carrying these past 30-some-odd years. He doesn't want to remember that he left the woman he loves for the joys of being eaten by an interstellar cockroach. Makes sense.
After Jay neuralyzes Kay, we flash forward a bit, and a tabloid headline informs us of his ultimate fate: He reunites with his wife after believing he'd been in a coma for 35 years.
Jay's story also comes full circle. He began the story as a young agent with untapped potential, and by its conclusion, he's come into his own as a fully competent agent. Through Kay's tutelage and his own latent skills, Jay's proven himself worthy to take up the torch, erm, neuralyzer.
We see Jay's transformation in his clothing as well. Although still dressed in sunglasses and a black suit, he has changed his suit to more reflect his personal tastes with a stylish mandarin collar and fit-over sunglasses. He informs Laurel, now Agent L, that Dennis Rodman is from Solaxium 9, demonstrating his transition from the student asking the questions to the teacher with the knowledge.
Jay and his new partner get into the car and metaphorically drive into the sunset. And roll credits… right? Wait, there's more?
Galaxy Quest
As Agents J and L drive away, the camera begins to zoom out. Our view retreats to see Manhattan Island, then the United States, and then the Earth. But it keeps going, taking us out of the Solar System, the Milky Way Galaxy, and even the universe.
The big reveal is that our universe is housed in a tiny glass ball, just like the one the Arquillians had. A giant alien—well, giant from our perspective—is playing marbles with our universe's ball and another housing a different universe. Picking up the two universes, he places them in a bag that houses even more universe marbles. Cut to black. Now we can roll the credits.
Besides being a nice surprise ending, the scene harkens back to something Kay said earlier in the movie:
KAY: Fifteen hundred years ago, everybody knew the Earth was the center of the universe. Five hundred years ago, everybody knew the Earth was flat. And 15 minutes ago, you knew that people were alone on this planet. Imagine what you'll know tomorrow.
Guess we'll just have to wit for the sequel.