This angered not only the aliens, but the Soviets as well, and slowed down the construction of their secret moon base. This in turn led to a whole chain of events that finally resulted in JFK saving the world from what he percieved as an alien infestation.
Thirteen years later, a second alien space craft arrived on Earth in search of the first, and to see if there were other survivors. They also switched the real JFK Jr. with an alien impostor.