In 1969 Agents J and the Younger K follow clues to first find Andy Warhol (an undercover agent), and then an alien with the gift to see all possible future timelines by the name of Griffin. Boris is also onto them, and when the Agents follow Griffin to Shea Stadium, Boris shows up and snatches him. The Agents give chase and scare him away, winning Griffin's trust who takes off his hat to reveal to them the Arcnet device to protect Earth from attack.
It needs to be launched into space, so they have no choice but to get to Cape Canaveral in a hurry by jet packs. They are arrested on site by a Colonel and his men, and tell the truth as a new tactic. It doesn't go down so well until Griffin shows the Colonel a vision of the future and he lets them through. Meanwhile both Future and Past Boris are also at the site, and try to stop the Agents putting the Arcnet device onto Apollo 11 which is set for launch.
Agent J manages to use some time travel of his own to defeat Future Boris by evading his spike weapons and pushing him off the launch tower. K shoots younger Boris' arm off, attaches the Arcnet to the shuttle, and gets out in time before launch. Older Boris is burned up as Apollo 11 takes off.
The Colonel is waiting for him, and Agent K is impressed with his new friend ... until suddenly young Boris shows up and kills the Colonel. K doesn't hesitate to shoot Boris dead.
At that time a car pulls up and a young boy gets out, asking for his father. Agent K gives him his father's watch, and we see now the young boy was Agent J. He then takes the boy under his wing. And no one seems to ask -- what was a 5 year old boy doing driving a car on a shuttle launch site???!
J goes back to the future now his job is complete, and meets K for pie at a diner -- and thanks his partner for looking after him. Griffin is also at the diner and tells us that this is his new earth story - except the one possible timeline where K forgets to tip, and an asteroid crashes into earth .... Except K returns, leaves the tip, and the asteroid hits a satellite instead.