It's a setup for an Undead Nightmare-style DLC featuring an alternate timeline in which aliens invade Los Santos shortly after the three protagonists meet, with many of the game's characters as antagonists working for the aliens.
As Michael is afraid of aliens, he goes AWOL immediately and serves as co-DJ of the revamped Blaine County Talk Radio, which is now exclusively used for Ron's segment, during which Michael's rambling makes Ron seem sane.
Lamar and Stretch join the alien forces, convinced that the aliens are working with the Illuminati.
Trevor, strongly opposing the Illuminati and various other pieces of conspiracy theorist bait, is the main force opposing the aliens. He also believes that the FIB agents are reptilians and kills them right away, pretty randomly.
Trevor and Franklin take over Fort Zancudo and set up a safe zone there, with the majority of the fort's population consisting of the many O'neill brothers. Trevor finds a jetpack and flies it around randomly in the background of every cutscene in which he isn't a featured character. Later in the story, a UFO attacks the base. Franklin tries to use the jetpack to stop the UFO, but immediately rockets into the sky and splatters against the underside of the UFO. In a cutscene afterwards, Trevor notes that the jetpack didn't have any weapons and would not have helped stop the UFO in any way, and Franklin died for nothing. He shrugs and walks out of the frame, and the remainder of the cutscene is a shot of the plain, corrugated metal hangar wall behind where Trevor stood. It continues for 23 minutes.
The final mission is Trevor killing Stretch and bringing Lamar to his senses, causing the aliens to agree to negotiate with Trevor. It is revealed that the aliens only wanted to probe Michael, and Trevor agrees to let the aliens sodomize Mike with their various devices.The final cutscene ends with Lamar comforting Michael, and Michael revealing that he liked being probed. Lamar sympathizes, and the two enter a homosexual relationship and move to San Fierro, setting up GTA VI.
The End.