The Marvel Cinematic Universe is already 18 films in. With the release of Avengers: Infinity War on April 27, the 19th film in the franchise, the MCU will be celebrating its 10-year anniversary. With more wins than misses, one would assume that the MCU is free of plot holes and other plot peculiarities. However, that is really not the case as the MCU is such a massive franchise.

In its long narrative timeline, there have been some plot threads that have been left behind in the MCU. Sometimes these unfinished plot threads go along to become fascinating mysteries, allowing fans to form rather interesting theories. Other times one wishes these plot threads were resolved, as many of them introduced many fabulous concepts and characters to the MCU that were never touched back upon in later films.

It is because the MCU has more wins than misses that there is an abundance of intriguing mysteries scattered around the wide Marvel landscape. These not only reside in the big screen side of the MCU, but also in the realm of television, such as in TV shows like Agents of S.H.I.E.L.D.and Netflix’s Jessica Jones.

With a wide variety of thrilling mysteries and unfinished plot threads in the Marvel Cinematic Universe, it would take a lifetime to list them all.

Nonetheless, here are the best 16 Mysteries and Plot Threads The MCU Has Left Hanging.

Lady Sif

We last saw Lady Sif up on the big screen in 2013’s Thor: The Dark World, where she aided Thor in protecting Asgard and the other realms from Malekith and his dark elves. She’s been one of the few cinematic characters to appear on Agents of S.H.I.E.L.D., where she guest starred on a couple occasions. But ever since her appearances on the TV show, she’s been absent from the big screen side of the MCU.

Jaimie Alexander was rumored to appear in last year’s Thor: Ragnarok, but due to scheduling conflicts with her hit show Blindspot, she unfortunately wasn’t able to make an appearance. Alas, this has left a huge plot issue in Thor’s narrative. Sif wasn’t mentioned or even alluded to in Thor: Ragnarok. This is rather odd considering how important she was becoming in The Dark World.

With Tessa Thompson’s Valkyrie being a wonderful new addition to the MCU, it would’ve been nice to have more than one female hero fight alongside Thor in Ragnarok.

15. Scarlet Witch and Quicksilver’s power source

Avengers: Age of Ultron showed us that Scarlet Witch and Quicksilver derived their powers from Loki’s Scepter, which housed the Mind Stone. This is why Scarlet Witch and Vision have a unique connection.

Nevertheless, this really doesn’t explain how Wanda and Pietro got their powers. With the pairing of Doctor Strange and Scarlet Witch in Avengers: Infinity War, it is believed that her connections to magic akin to her comic book counterpart will be explored in the film. Perhaps they always had superpowers that were triggered by the Mind Stone that unlocked their hidden X-type gene, due to trauma during Baron von Strucker’s experiments.

Hopefully such revelations will be revealed soon. Or, if the Disney-Fox deal is approved by the government, Marvel can finally officially call them mutants. The comics have constantly altered Scarlet Witch and Quicksilver’s origins, but it’s a given that many fans would rather call them mutants.

The Ten Rings and the Mandarin

The Ten Rings terrorist organization was established in the first Iron Man film. They made a comeback in 2013’s Iron Man 3, where it was revealed that the Mandarin was actually the actor Trevor Slattery. This definitely angered some fans so Marvel followed the film with the short All Hail the King. Here, it was established that the Mandarin does indeed exist in the MCU. That’s great and all, but we haven’t heard of the Ten Rings or the Mandarin since the short’s release.

Being that the organization is very important to Tony Stark’s narrative, it seems a bit strange that we haven’t heard of them since. There was a deleted scene in 2015’s Ant-Man where a Ten Rings member attempted to buy the Yellowjacket suit, but that’s not even canon. Hopefully the Mandarin will make his formal debut in Phase 4.

Black Widow and Hawkeye’s past

Perhaps one of the biggest mysteries in all of the MCU concerns Black Widow and Hawkeye’s past.

A constant question in many Marvel fans’ minds is what happened in Budapest?

Back in 2012’s The Avengers a lot of emphasis was put on Black Widow’s tainted ledger, as well as her connection to Hawkeye. One scene in particular showed the two spies shooting it out it in what is supposedly their mission in Budapest, Hungary. After The Avengers, though, this plot thread was completely abandoned.

We haven’t heard of the notorious Budapest mission since 2012, much less about how Black Widow and Hawkeye became who they are today. With a Black Widow movie supposedly in the works, hopefully we’ll finally see what happened in that secret mission to Budapest.

Heimdall’s Eyes in Age of Ultron

There’s a scene in Avengers: Age of Ultron that’s both loved and hated by fans. That’s the infamous Thor bath scene where the god of thunder gets a vision. This vision shows Heimdall without his orange eyes. This scene led fans to speculate that Heimdall had the Soul Stone and that it was because Thanos would take it away from him that his eyes were now white.

Many films later, we still don’t know what that scene means.

Heimdall’s eyes were still orange in 2017’s Thor: Ragnarok and it looks like the Soul Stone is in no way connected to Heimdall at all. For now it’s looking like Heimdall’s white eyes are a mystery that will keep on going. Or maybe this mystery will finally be resolved in Avengers: Infinity War.

The Red Skull’s whereabouts

Remember the Red Skull? The Captain America villain made his first and only MCU appearance in Captain America: The First Avenger. We haven’t seen him since. He was briefly shown in a Hydra montage during the Arnim Zola scene in Captain America: The Winter Soldier, but other than that, he’s M.I.A.

We know that he is not dead since the Tesseract took him somewhere out in space. What we don’t know is exactly where he went.

Many fans speculated that like Thor in Ragnarok, Red Skull perhaps ended up in Sakaar, Grandmaster’s planet. Others even theorized that Red Skull is actually Thanos. The latter is definitely one of the most creative theories out there, but it totally shows just how much fans want to see Red Skull return.

The Leader and Abomination

The Incredible Hulk is one of the most obscure films in all of Marvel, and just as obscure are the villains it introduced: the Leader and Abomination. These two Hulk villains haven’t made an appearance, nor a cameo, nor have they even received a mention since the aforementioned Hulk movie. We know that Abomination survived the fight in Harlem against the Hulk.

The Leader was teased near the end of the movie.

For now, it seems they will not be making a future appearance in the MCU. Marvel Studios president Kevin Feige is not opposed for them returning, but with the MCU going cosmic, it’s not looking likely. Alas, the hard truth is that these characters will probably never return, but we can always keep hoping.

Who hired Crossbones in Civil War?

Captain America: Civil War’s plot is full of convenient coincidences. For example, despite how incredibly good the film is, it’s almost absurd how many events and character decisions had to fall into place for Iron Man, Captain America, and Bucky to end up in Siberia by the end of the movie. The first convenient plot moment, though, happens right in the beginning of Civil War.

When Crossbones is about to blow himself up, Cap hesitates to apprehend him due to Crossbones mentioning Bucky. From there on, the plot takes its course. Looking back, one would assume that Zemo had orchestrated Crossbones’ terrorist scheme to provoke Cap, but that’s simply not the case at all. We actually don’t know why Crossbones wanted to steal the biochemical agent from Lagos, or who hired him in the first place.

In fact, the whole Crossbones plot thread was never revisited in the film, leaving us with more questions than answers. Was it the Mandarin that hired him? Or the now-defunct Advanced Idea Mechanics?

What happened to A.I.M.?

We last heard of Advanced Idea Mechanics in 2013’s Iron Man 3. The company, founded by Aldrich Killian, developed the Extremis virus with the help of Maya Hansen. Aldrich later used it to manipulate the arms race by creating the persona of the Mandarin.

Tony Stark eventually defeated him, and that was the last we heard of Aldrich and the company.

Unlike Hammer Tech, which was introduced in Iron Man 2 and made a notable resurgence in Netflix’s Luke Cage, A.I.M. has seemingly been left behind in the MCU.

Some fans have speculated that Tony perhaps acquired the company. Another theory is that A.I.M. were the ones who hired Crossbones and perhaps also gave him Extremis-like abilities. Whatever the case may be, it’s about time A.I.M. returns to the fold - if not in the main line of movies, then maybe in one of Marvel’s many TV shows.

Ultron’s fate

Avengers: Age of Ultron saw the introduction of Ultron in the MCU. By the end of the film, it is hinted that Ultron is perhaps still alive after Tony destroyed all the Iron Legion robots. As you might recall, the last Iron Legion was supposedly disintegrated by Vision.

A widely-accepted theory among fans is that Vision actually trapped Ultron within the Mind Stone.

Interestingly, Ultron has been referenced many times in the many MCU films that came after Avengers 2. An Ultron head was even present in Spider-Man: Homecoming. With all these callbacks to Ultron, one can only wonder whether he will actually ever return. If he’s really hiding within the Mind Stone, then perhaps such a reveal will be handled in the upcoming Avengers: Infinity War.

The Celestial Family Tree

We were formally introduced to the Celestials in the MCU in 2014’s Guardians of the Galaxy. The first to wield the Infinity Stones, these beings are immensely powerful, and surprisingly, we’ve seen quite a few of them in the MCU.

This begs the question: how important are they to the overall MCU narrative?

So far, we know Ego the Living Planet, the Collector, Grandmaster,  and Peter Quill/Star-Lord all belong to the Celestial race. Which itself begs another question: are they all related? This is definitely a fascinating query and one we’ll hopefully get some answers to in Guardians of the Galaxy Vol. 3. For now, we can only speculate, but it’s looking like a Celestial family tree is coming to fruition.

Nick Fury’s eye

The mystery behind what happened to Nick Fury that caused him to lose his eye is one that’s been around since Iron Man’s post-credit scene. We got a hint in Captain America: The Winter Soldier when Fury mentioned that “the last time I trusted someone, I lost an eye.” Since Samuel L. Jackson is set to appear in 2019’s Captain Marvel as a young Nick Fury, then perhaps we’ll finally see what truly happened.

It’s possible that the person Fury trusted was Carol Danvers (Brie Larson), or maybe even Mar-Vell, who’s also set to appear in Captain Marvel, played by Jude Law. It’ll definitely be interesting to see how Fury lost his eye, but more interesting will be how it all connects to the wide MCU narrative going forward.

Graviton

One of the most interesting plot threads left behind by Agents of S.H.I.E.L.D. was the Graviton storyline from season one. Indeed, we haven’t heard of Dr. Franklin Hall/Graviton ever since. Perhaps, though, he will return on this fifth season of the show. Especially since gravitonium has become a central plot element this second half of the season.

Since this season might also be Agents of S.H.I.E.L.D.’s last, then maybe Graviton will be the main big bad of the show. That will definitely explain the show’s mystery on who or what destroyed the Earth in the future. It was thought that Quake was the one responsible for such a catastrophe, but perhaps the show is setting us up for Graviton’s spectacular comeback. If so, it would definitely end the show with a huge bang.

The Raft

The Raft, the underwater maximum security prison, was introduced in Captain America: Civil War. It was there that Team Cap was sent after the airport battle in Civil War. The Raft was later mentioned in season two of Netflix’s Jessica Jones. Here, Jessica’s mother was going to be sent to The Raft due to her superhuman strength.

It seems then that the Raft is a widely known location to the public in the MC,U akin to how many Americans know of the infamous Guantanamo Bay prison. If so, then what supervillains are currently aboard the Raft? This is one mystery that has many fans overly speculating.

One name that usually comes up in theories is Abomination, who we last saw in The Incredible Hulk. There’s really no way to know, but with the Raft’s mention in Jessica Jones, then perhaps we’ll be hearing more of the Raft in Daredevil season three or Luke Cage season two.

How Agent Carter created S.H.I.E.L.D.

Many fans were disappointed when ABC canceled Agent Carter after just two seasons. The TV show was heavily praised by fans, but unfortunately low viewership led to its cancellation. This left many plot threads unfinished, with the biggest mystery being how Peggy Carter went from working as an SSS (Strategic Scientific Reserve) agent to eventually founding S.H.I.E.L.D.

Petitions were made and many fan letters were written to companies such as Netflix to revive the show, but to no success.

This is a plot thread that will either be left to Agents of S.H.I.E.L.D. or a future MCU movie to solve. Peggy went along to make one more appearance in the MCU after her TV show was canceled. She appeared in Captain America: The Winter Soldier, before she passed away in Civil War, of old age.

The Soul Stone

The biggest mystery of them all: where (or when) in the MCU is the Soul Stone? It’s the most theorized concept in all of the MCU, leading to a plethora of fan theories that have dominated the internet for almost a decade. Even Infinity War directors Joe and Anthony Russo have joined in the fun with their hashtag #whereistheSOULSTONE.

One of the most prominent Soul Stone theories is the T.H.A.N.O.S. theory, which says that each Infinity Stone is contained within an object whose name start with one of Thano’s letters. This has led many fans to speculate that the Soul Stone is within Heimdall or Hela, since “H” is the only letter left to fill.

Another very interesting theory is the Time Travel theory, which makes us question not where the Soul Stone is, but when in time it could be. Whatever the case may be, the decade-old question is set to be answered in Avengers: InfinityWar.

What other plot threads has the MCU left hanging? Let us know in the comments.

  • Guardians of the Galaxy Vol. 3 Release Date: 2023-05-05 Avengers: Infinity War Release Date: 2018-04-27 The Avengers 4 Release Date: 2019-04-26 captain marvel Release Date: 2019-03-08 Ant-Man 2 Release Date: 2018-07-06