UFOs

Four different UFOs have been found so far, three of them requiring 100% game completion in order to see them.

Mount Chiliad UFO
A UFO with FIB markings on it can be found at the peak of Mount Chiliad.

Requirements: Once all of these conditions are met, the UFO appears. It behaves differently from the other UFOs in the game - it only appears when the above conditions are met, and if you leave the viewing platform it temporarily disappears until you walk back to the platform.
 * 100% Game Completion
 * Rain (storming or not)
 * 3 AM
 * Stand on the viewing platform

It's been speculated that the UFO might be bugged because of its odd behavior that almost seems like it's glitching and isn't doing what it's supposed to. Seeing as no real progress has been made in the mystery in a very long time, this is quite possible.

Procopio Beach - Sunken UFO
A sunken UFO that is very similar to the FIB UFOs can be found in the northern part of the map off the coast of Procopio Beach, only accessible with scuba gear or a submarine. The only interesting thing about this UFO is that it seems to share the same model as the FIB UFOs, but it doesn't have FIB written on it. It's possible that this UFO is a prototype or even an actual alien spaceship.

This is the only UFO that can be found without 100% game completion and because of that probably isn't related to the mystery and is just an easter egg.

Alien Camp UFO
Another UFO with "FIB" written on its side can be found above the Alien Camp in Sandy Shores, near the maximum altitude you can fly.

A beam opens up on the bottom of the UFO every few seconds, and many have tried to fly into the UFO while the hatch is open but no one has succeeded.

Flying near the UFO causes your screen to distort and beaming sounds trigger, and then your helicopter or plane's engines will cut off. This makes it hard to land directly on the UFO but it's still possible, but standing in the center of the UFO will launch your character into the air.

Fort Zancudo UFO
Directly above a bunker in Fort Zancudo, a black UFO can be found at around 70-80% of the maximum height.

This UFO looks very unique and has a strange group of orange... things on the bottom that move around.

Green lights (assumed to be from the UFO) shine down on the bunker in Fort Zancudo between 1 and 4 AM which get the most intense at 3 AM. These lights are what led to the UFO being discovered.

Similar to the Alien Camp UFO, this UFO will cut off the engines of your vehicle if you get too close, and it makes a distinct screaming sound when this happens. The UFO also constantly emits a strange electronic noise as long as you're close enough to it.

Alleged UFOs
None?