The heavily guarded military base found in Blaine County, Fort Zancudo, holds many a secret. Much like the Area 69 base in GTA: San Andreas which hid the Jetpack, there is more to GTA V's only military establishment than meets the eye.
One Youtuber decided to try uncover the military secrets housed in the base and share his findings with the GTA V community. While most of this is just conjecture, keep in mind that mere conjecture has lead to the discovery of several GTA secrets in the franchise's past, and that conjecture is what keeps revealing newer and newer clues regarding the Mount Chiliad mystery, which remains unsolved to this day.
In a fashion similar to that of Area 69, Fort Zancudo will only ever appear on your map if you've actually, physically been there. Only a single mission in the single player story sees players entering the fort, it being closed of at all other times, which increases the air of secrecy surrounding it. Several of the fort's facilities suggest that it has some special purpose, including a school of sorts.
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The marines housed in the fort perform daily military routines, many of which aren't standard procedures, and the entire base seems to be active, as if it assumed that an active war was going on (considering the amount of havoc certain GTA V players can cause, this suddenly does not seem so outlandish). Another notable mystery is the fort's connection with the previously mentioned Mount Chiliad mystery, which also involves the elusive UFOs of GTA V. One such UFO can be seen directing its tractor beam onto the underground bunker in the Fort under certain circumstances, lending the area its characteristic green glow. It is entirely possible that Fort Zancudo might hide the solution to the Chiliad mystery, but that particular info is still top secret.
Are you intrigued by the various mysteries GTA V is filled with?