The Agents of S.H.I.E.L.D. season 6 premiere set up a mysterious plot with higher stakes than ever before - and here are all the key questions that will be explored over the rest of the season. Agents of S.H.I.E.L.D. is the Marvel TV series that continually reinvents itself, with each season adapting to work in different themes and concepts. Season 4 blended the supernatural horror of the Ghost Rider with the sinister virtual reality of the Framework; season 5 was a sci-fi adventure that, frankly, did time travel better than The Flash.

Agents of S.H.I.E.L.D. season 6 is heading in a very different direction, jumping just over a year forward in time. Over on Earth, Mack has established himself as director of S.H.I.E.L.D., and he rebuilt the organization from the ground up. Meanwhile, another group of S.H.I.E.L.D. agents are out in space, in an epic adventure that feels more like The Expanse than anything the S.H.I.E.L.D. team has dealt with before. And a new threat is stepping out of the shadows - one with a very familiar face.

Related: How Agents Of SHIELD Season 6 Addresses Thanos' Snap & Endgame

A season premiere is really all about setup. As a result, the Agents of S.H.I.E.L.D. season 6 premiere, appropriately entitled "Missing Pieces", raises a lot more questions than it does answers. As long-term viewers will know, Agents of S.H.I.E.L.D. delights in complex, long-form storytelling - the mystery of the broken Earth ran through the entire fifth season - so it's safe to say that answers will not be provided at speed. But what questions, exactly, are raised by "Missing Pieces"?

12. How Does Agents of S.H.I.E.L.D. Fit Into the Wider MCU?

Agents of S.H.I.E.L.D. has always been on the periphery of the Marvel Cinematic Universe, carefully tying into the movies - whether through specific events, as in season 1, or through thematic nods such as the introduction of the supernatural to coincide with the release of Doctor Strange. Unfortunately, the sheer cosmic scale of recent events in the movies have caused significant problems for the show. Season 5 technically ended at the very same time as the events of Avengers: Infinity War, and season 6 is ostensibly set a year later, but the showrunners have admitted they have no intention of dealing with the Decimation. There's a simple reason; communication isn't quite good enough between Marvel Studios and Marvel Television, so S.H.I.E.L.D.'s writers had no way of knowing what the post-Decimation world was supposed to look like.

Co-showrunner Jed Whedon has insisted that Marvel do have something worked out to explain this, but they're in no hurry to spell it out. For now, it looks as though Agents of S.H.I.E.L.D. is back to thematic ties; Spider-Man: Far From Home looks set to explore the Multiverse, and Agents of S.H.I.E.L.D. season 6 seems to involve interdimensional travel. That may well ultimately explain why the show is ignoring the snap; perhaps all the time travel in season 5 created an alternate timeline in which Thanos never triumphed, and Agents of S.H.I.E.L.D. takes place in that reality.

11. What are the "Reality Warps?"

Agents of SHIELD Season 6 Clark Gregg

The S.H.I.E.L.D. team have been tracking down so-called "reality warps," areas where the fabric of reality appears to become thin enough to allow portals to open between one place and another. The effects are reminiscent of the Convergence from Thor: The Dark World - complete with a flock of birds who emerge from the ground at one point - and beings are able to jump through the portals, an experience that is referred to as a "crossing." Although S.H.I.E.L.D. believes the reality warps are artificial, they may be a natural event, with mysterious forces from another world (or dimension?) taking advantage of them. Certainly they don't appear to be particularly safe.

Related: How The Thor Movies Secretly Introduced The Multiverse To The MCU

Agent Keller speculates that the reality warps are all happening along ley lines, a mythological idea that ancient sites of power are somehow distributed along lines of energy that crisscross the globe. In the real world, ley lines are typically viewed as pseudoscience, but the MCU is a reality where the Norse gods are really a race of ancient aliens, so it looks as though Keller is right. Presumably the ley lines either mark locations where the fabric of reality is vulnerable, or else the mystical energy is being tapped into in order to make the crossings.

10. How Long Have the Reality Warps Been Going On?

It's implied that these reality warps have been going on for several months, long enough for the S.H.I.E.L.D. team to begin identifying a pattern but not long enough for them to start predicting the next site. Mack has organized his resources by sending strike teams across the globe for fast response when a crossing is detected.

9. Who is Clark Gregg's New Character, and What is he Doing on Earth?

Phil Coulson may have died, but Agents of S.H.I.E.L.D. season 6 kicks off with the introduction of a brand new character - one who shares Coulson's face. Referred to as "Sarge," Not-Coulson is leader of the mysterious band of mercenaries who have crossed through the reality warps. "Missing Pieces" doesn't even try to explain Sarge; in fact, it doesn't show much footage that wasn't teased in the trailers.

8. What's Happened To Fitz?

Meanwhile, in space, Simmons, Quake, Davis and Piper are the last four S.H.I.E.L.D. agents still looking for Fitz. It seems it took them a while to reverse-engineer Confederate technology in order to create wormholes through space, and in that time, the spaceship Fitz and Enoch were in was attacked. Fitz has been revived from cryostasis, and is apparently working for a mysterious Controller.

Related: Agents of SHIELD Theory: New Coulson Is From An Alternate Dimension

It's unclear what happened to Enoch, the Recorder who was watching over Fitz. Even more mysterious is the question of just why this didn't happen in the original timeline, the one where Earth was destroyed. That fact strongly suggests the Confederacy are involved in this somehow.

7. Why is the Confederacy Hunting for S.H.I.E.L.D.?

The S.H.I.E.L.D. team has made a name for itself over the last year or so, with Quake insisting that alien races have to see the handful of humans as strong enough to be a threat. Unfortunately, Daisy's approach seems to have meant S.H.I.E.L.D. hasn't made any friends, but rather a whole lot of enemies. The Confederacy seems to be hunting S.H.I.E.L.D. down, and in one scene when they identify the S.H.I.E.L.D. ship, they open fire, attempting to destroy it. This may simply be an attempt to get back at S.H.I.E.L.D. after season 5, when Graviton killed the Rajak leader and S.H.I.E.L.D. crossed the Remorath and the Kree. But it's also possible that S.H.I.E.L.D. has caused a lot of problems for the Confederacy over the last year.

6. How is S.H.I.E.L.D. Traveling Through Space?

In Agents of S.H.I.E.L.D. season 5, the S.H.I.E.L.D. team discovered that Hydra had secretly owned a device to open small-scale portals through space. This was actually Confederate technology, and it looks as though S.H.I.E.L.D. has successfully reverse-engineered it; they can use these portals to jump across vast tracts of space.

This method of cosmic transportation is very different to the one used by the Guardians of the Galaxy. Visually, it's a little more reminiscent of the portals opened by the Tesseract; it may even be that this device uses Tesseract energy, given Hydra recovered their portal device in 2012, after the Battle of New York in The Avengers.

Related: The Tesseract Has Appeared In More Marvel Movies Than Captain America

5. How canS.H.I.E.L.D. Understand Alien Languages?

Presumably the S.H.I.E.L.D. team has picked up some of the alien translators that are apparently common in space, and are used by the Guardians of the Galaxy. These translators don't work on written script, though, and Simmons has devoted some of her time over the last year to learning how to read some alien languages, too.

4. Just How Powerful is Quake After Season 5?

Chloe Bennet Agents of SHIELD Season 6

In Agents of S.H.I.E.L.D. season 5, Quake was injected with the Centipede Serum in order to expand her powerset so she could defeat Graviton. The effect seems to have been permanent, and in the season 6 premiere Quake demonstrates a greater degree of control over her abilities than she's ever shown before. She's literally able to vibrate apart three energy weapons without the aliens holding them seeming to feel anything.

In the comics, Quake has been described as an "Omega Level" superhero, meaning her powers theoretically have no limit. That fits with Agents of S.H.I.E.L.D. season 5, where in an alternate timeline Quake's stolen powers were able to crack the planet Earth like an eggshell. It will be fascinating to see just how powerful Quake now is.

Related: Quake Could Be More Powerful Than Ever After Agents of SHIELD Season 5

3. Why are Yo-Yo and Keller Keeping their Relationship Secret?

The Agents of S.H.I.E.L.D. season 6 premiere introduced a new S.H.I.E.L.D. agent, Keller, and swiftly revealed that he's secretly in a relationship with Yo-Yo. It seems Mack withdrew emotionally as soon as he became director, and Yo-Yo has finally decided it's time to move on. For some reason neither she nor Keller are willing to make this public knowledge, although May suspects.

Related: Agents of SHIELD Season 6 Could See The Return of the Kree - Here's The Evidence

2. Who is Doctor Benson?

"Missing Pieces" also introduced Doctor Benson, brought in by May in order to set up the new S.H.I.E.L.D. Academy and act as a scientific adviser in the absence of both Fitz and Simmons. Benson is an old colleague of May's ex-husband Andrew Garner, and works as a lecturer at Culver University. Attentive viewers will recognize Culver University as a site visited in The Incredible Hulk; Marvel Television seem to like name-dropping the institution, which has been referenced in Runaways as well.

1. Who is The Controller?

Artwork depicting the Controller

The Agents of S.H.I.E.L.D. season 6 premiere ended with a brief glimpse of Fitz, revealing that he's working for a mysterious figure known as "The Controller." In the comics, The Controller is an Iron Man villain who mastered slave discs with which he binds people to his will. Although he's a human, he's wound up working with several alien beings in the past, including Thanos himself. This may be an entirely different character, of course; "Controller" is a title after all, and the episode doesn't show any hint of slave discs.

More: Marvel Already Did Captain Marvel's Story (But Better) on Agents of SHIELD

Agents of S.H.I.E.L.D. season 6 airs Fridays at 8pm on ABC.