With over a quarter-century of background lore for players to sift through, the Fallout series is known for having exhaustive amounts of information on most subjects. That said, there are also plenty of areas in the wider lore that lack a thorough explanation for one reason or another. Sometimes this is accidental but in other cases, it's by design.
For the latter, the idea is that the best way to build up intrigue and tension is by shrouding certain things in mystery. In essence, not explaining something and letting the mystery circulate among fans is simply more fun. Here are a few of the most well-known unsolved mysteries of the Fallout universe.
7 The Institute's True Objective?
By the end of Fallout 4 players become intimately familiar with the Institute's actions throughout the wasteland. They are the ones responsible for synths (as well as using them to replace key members in the Commonwealth's settlements) and are even behind the super mutant presence in the region.
What players never really figure out, however, is their end goal. What is it exactly that the Institute wishes to gain by doing things like this? When pressed, they claim they're working toward the benefit of humanity, but this is an extremely vague answer.
6 Who Is The Mysterious Stranger?
This one is not likely to be answered with any depth in the near future, but that hasn't stopped Fallout fans from speculating on the identity of the Mysterious Stranger character. For those still unaware, the Mysterious Stranger is a character who will randomly appear while in VATS and kill the enemy the player has targeted. This only happens if the player has the Mysterious Stranger perk.
The closest players get to learning his identity is in Fallout: New Vegas where it is strongly implied that he is the father of the Lonesome Drifter. Nothing more than this is known.
5 The State Of The Wider World
Given that Fallout games have only been set in America so far, no one really knows what the rest of the world looks like after the Great War of 2077. Some characters like Allistair Tenpenny are obviously foreign, though he really doesn't go into detail about the state of his homeland after the bombs dropped, although it can't be that great given the fact that he immigrated to the Capital Wasteland of all places seeking opportunity. The intro slides of each game indicate that most of the planet was decimated by nuclear weapons, however, nothing more is really known at this point.
4 What Do The Aliens Want?
Aliens have been present in nearly every Fallout game, but players are no closer to discovering their motives now than they were twenty-five years ago when they first appeared in the first Fallout as an easter egg. While Fallout 3's Mothership Zeta DLC gives the clearest picture of them as well as their technology, not much is gleaned about what they're doing on Earth, although one holotape seems to indicate that they were interested in nuclear codes before the Great War.
Whether they're the ones responsible for the bombs dropping is currently unknown (and unlikely). Perhaps their presence on and around the planet is motivated by mere scientific curiosity.
3 Who Started The Great War?
While President Dick Richardson in Fallout 2 claims that it was the Chinese who first emptied their missile silos, he is hardly the pinnacle of truth in which players ought to place their faith. What is known is that America and China were involved in a conventional armed conflict just minutes before the bombs were launched, with both sides having a reason to launch the missiles as either a preemptive strike or as a retaliatory measure. The Vault Dweller has the best perspective on this question, however - it doesn't really matter anymore, does it?
2 What Became Of The Vault Dweller / Chosen One / Lone Wanderer?
For one reason or another, there's not much known about what happens to the player characters of Fallout1, 2, and 3. The Vault Dweller has the most post-game information available for the player to learn, however after a certain point he is said to have disappeared from Arroyo and was never found. Fallout 2's Chosen One went on to rebuild Arroyo with the former residents of Vault 13, however, nothing beyond this is known in the canon.
Much less is known about the Lone Wanderer from Fallout 3, who isn't mentioned in any subsequent game, nor is any indication of his fate given in the game's ending slides. The Official Game Guide for Fallout 3 mentions some things about him but the canonicity of this is up for debate.
1 What's Going On With The Dunwich Cult?
The Dunwich Cult is one of the weirdest aspects of the Fallout universe. Not only are they an overtly paranormal element in what is concretely a sci-fi franchise, but not much is also known about them. What is known is that they pray to one being (among possibly many) named Ug-Qualtoth and that the cult has many front organizations that are used to cover their occult behavior.
Little is known about either the meaning behind this occult behavior or its endgame. Why did they perform human sacrifices? What is the meaning behind their tributes? Perhaps the next Fallout will reveal more about them...or maybe it won't.