Fallout 4 is a huge game, packing hundreds of quests, characters, and lore into its open world. And while most stories encountered by the Sole Survivor have solid endings, although not always happy ones, there are others that are a little more of a puzzle. Not everything in the post-apocalyptic Commonwealth can be easily wrapped up or explained, leaving no shortage of mysteries for fans to solve.

There are plenty of strange quests in Fallout 4, with many quirky NPCs, locations, and creatures that leave a lasting impression on the Sole Survivor. However, with odd supernatural forces and technology run amok, there is also a plethora of phenomena that defy explanation. The biggest mysteries in the Commonwealth can leave even the most insightful Sole Survivor scratching their head.

10 Are The Commonwealth's Mannequins Alive?

Many Theorize These Dummies Have Minds Of Their Own

One fun unsolved mystery involves the many mannequins that can be found throughout the Commonwealth. These former department store displays can be stumbled upon by the Sole Survivor in some very unlikely places and often in creepy situations. While it is possible that posing the mannequins has become a post-apocalyptic hobby for some, there's also the explanation that the dummies could be alive or are perhaps haunted.

The Far Harbor DLC features a shipwreck off the coast to the southwest of the Island near Fringe Cove Docks. This wreck is filled with mannequins that seem to confirm that theory, with the crew complaining about weird noises. If the Sole Survivor investigates the sunken vessel, various clues seem to point to the mannequins being responsible for the ship sinking and the crew's demise, but with no clear answers, it’s left to the imagination.

9 Does Mama Murphy Really Have Visions?

Real Fortune Teller Or Crazy Old Lady?

Mama Murphy is an iconic Fallout 4 character, with her fluffy slippers, big earrings, and trademark headscarf making her instantly recognizable. As soon as the Sole Survivor meets her in Concord’s Museum of Freedom, Mama Murphy will start giving them advice based on the 'Sight', a strange precognitive power she claims she has. And while Mama Murphy's visions are helpful, there is never any clear evidence that she is psychic.

There are other examples of clairvoyants in the Fallout universe, such as Bloomseer Poplar in Fallout 3 and The Forecaster in Fallout: New Vegas, who was in turn inspired by the psykers seen in the first Fallout game.

Many theories could explain Mama Murphy's powers. The most common and obvious theory is that she is simply tripping from her heavy chem usage, something that can cause her death in Fallout 4. However, other theories run from her being a former Institute employee to her possessing or coming in with an artifact similar to Lorenzo's crown or a malfunctioning Gen 3 Synth.

8 What Was The Institute’s End Goal?

'Mankind, Redefined' Sounds Good, But What Does It Mean?

The Institute acts as Fallout 4's primary antagonist, although there is the option to their side later in the main quest. As such, much of what they do is framed through the eyes of the people of the Commonwealth, who live in fear of the technologically superior faction and their shadowy goals. However, once the Sole Survivor actually meets the Institute, those goals don’t become any clearer.

Everyone in the Institute’s underground base will repeat that what they are doing is for the betterment of mankind, but no one seems to really explain what that means. As they kidnap people, destroy settlements, and churn out more and more Gen 3 Synths, there is never any real indication that they are making anything better. While there are many theories in the fanbase about the Institute’s objectives, perhaps one of the better ones suggests that the scientists forgot long ago and are simply repeating the mantra as they follow their orders.

7 Why Is Vault 101 Gear In Covenant?

How Does The Town Connect To The Capital Wasteland?

Venturing into the settlement of Covenant, the Sole Survivor will immediately notice something different about the remarkably preserved town. Investigating further will draw them into an ethical dilemma regarding experiments on Synths, and they will have to choose between Honest Dan and Dr. Chambers during the quest “Human Error”. However, during this quest, while navigating the maze of rooms inside Chambers’ compound, there is evidence that seems to tie Covenant to Vault 101.

Vault-Tec motivation posters can be found throughout the compound, all with Vault 101 Vault Boys, along with recolored Vault-Tec security uniforms for the guards. Comparing the posters to those found in Fallout 3, some subtle differences indicate that these were specifically made for Fallout 4 rather than being reused assets. But why a settlement in the Commonwealth would have Vault 101 equipment is never addressed, leaving room for almost a decade of speculation.

6 Is Kellogg Still In Nick's Head?

Can Nick Ever Be Fully Trusted Again?

As part of the main questline mission "Dangerous Minds", a piece of Kellogg's brain is implanted into Nick Valentine, allowing him and the Sole Survivor to explore the mercenary's memories. As well as providing new insight into Kellogg, this quest is how the Institute's teleportation technology is revealed, moving Fallout 4's plot forward. However, at the end of the quest, there is a strange moment as Kellogg briefly speaks through Nick, which raises so many questions.

Kellogg still being in Nick's mind was part of a cut quest, but leaving this piece in was a deliberate choice, making the whole moment all the more jarring. What makes it worse is that Nick seems to have no knowledge of Kellogg hijacking his voice and the whole thing is brushed aside. Cut content aside, it leaves Nick's loyalty and stability in question with the unseen threat of Kellogg potentially lurking in his mind.

5 Why Did The Institute Kill Everyone In Vault 111?

It Seems Like A Waste Of Potential DNA

During Fallout 4's opening sequence, after being frozen in the cryo pod, the Sole Survivor will briefly wake up just in time to see their spouse murdered and their son taken by Kellogg and the Institute. Waking up once more decades later, they can then learn the true horror of that day, as it becomes obvious that all the residents of Vault 111 are dead. However, it is never explained why all the other frozen people were woken up, let alone allowed to suffocate in their pods.

Even Kellogg will comment in "Dangerous Minds" that he never understood why the Institute let the others die, with his guess being they were potential loose ends. But that also makes no sense, as even the residents in other rooms were killed, and they would never have seen the Institute team. Whatever the Institute's reasons, it serves as an early example in the game of their callousness towards human life.

4 Who Or What Is The Mother Of The Fog?

Could She Truly Be An Otherworldly Being Or A Devoted Cult Member?

The Far Harbor DLC has some of the most interesting locations and quests as the Sole Survivor explores the Island and meets new factions. One such faction is the Children of the Atom, who will require the Sole Survivor to go on a vision quest before they can . This will begin the quest "Visions in the Fog," and the ghostly Mother of the Fog will appear to guide the way to the shrine.

There are several theories surrounding the Mother, with the strongest linking the phantasmal figure to a hermit on the Island who uses Stealth Boys. However, there are also those who believe she is a hallucination brought on by the radiation, taking the form of a woman in people’s minds as the myth of the Mother grows. The continued supernatural elements in the Fallout series could also mean that the Mother is a spirit or ghost, but the game never confirms anything one way or the other.

3 What Was Going On At Dunwich Borers?

So Little Is Known About The Strange Cult

Dunwich Borers is a location in the northeast of the Commonwealth, directly east of the Slog and the Saugus Ironworks. At first glance, it appears to be nothing more than a quarry overrun with raiders, but as the Sole Survivor delves underground, strange noises and flashbacks start to happen. These will gradually become more disturbing until an altar can finally be found underwater at the very bottom.

The Dunwich Borers quarry links with the Dunwich Building, a Fallout 3 location likewise owned by Richard Dunwich and his company Dunwich Borers LLC that also features strange phenomena, audio logs, and very creepy ruins. The flashbacks show rituals and sacrifices taking place pre-war, hinting at cults in the United States who worshiped eldritch entities. But just how widespread this was, and what their goals were, has yet to be explained.

2 Where Is Dr. Zimmer?

How Could A High Ranking Institute Member Go Missing?

First met in Fallout 3, Dr. Zimmer is a high-ranking member of the Institute who will enlist the Lone Wanderer's help in tracking a fugitive Synth. Zimmer, at this time, is the head of the Synth Retention Bureau (SRB) of the faction and has traveled to the Capital Wasteland in person to search for the missing Synth. However, by the time Fallout 4 takes place, 10 years later, Zimmer is missing, with Dr. Ayo running the SRB.

If killed in Fallout 3, Zimmer will drop an android component similar to the Synth components seen in Fallout 4.

While it could be easy to assume an elderly man like Zimmer could have ed away, this doesn't seem to be the case, as he is listed as missing by the Institute. If asked about it, Ayo will state that Zimmer was supervising the retrieval of high-profile units, making it sound like a mission gone wrong. Unsurprisingly, there are plenty of theories, such as the high profile units were all former Coursers, and given the role they play within the Institute, it makes sense they would want to keep Zimmer's mission and fate a secret.

1 Who Or What Is The Mysterious Stranger?

The Man, The Myth, The Legend

Finally, no discussion about Fallout mysteries would be complete without mentioning the Mysterious Stranger. First appearing in the original Fallout game, this enigmatic man has gone on to pop up in every Fallout release. In his iconic trench coat and fedora, the Mysterious Stranger lends his aid during combat, although the mechanics of how he does so have changed over the years.

As the name suggests, this helpful gunslinger's true identity is a mystery, with fan theories ranging from time traveler to Synth to alien. For the Mysterious Stranger to appear in Fallout 4, the perk of the same name must be chosen, allowing him to help out the Sole Survivor in V.A.T.S. Amusingly, while most characters throughout Fallout do not acknowledge the Mysterious Stranger, Nick Valentine is fully aware of him and even has a full dossier on the Stranger in his office.