Marvel’s Agents of S.H.I.E.L.D. has now finished its freshman season on ABC and while the series started on the wrong foot and met harsh criticisms, the tie-ins to Captain America: The Winter Soldier and resulting game-changing events righted the ship. As a result, Agents of S.H.I.EL.D. finished relatively strong (read our review), earned back a lot of respect from fans, and better yet, won itself a second season order.

With the final stretch of the season running with the tagline “it’s all connected,” did the series deliver on that notion? Let’s take a look at some critical questions raised throughout the 22 episodes and ask a few more that remain unanswered as we say goodbye for now to Agent Phil Coulson and his team.

*Warning: This post contains major spoilers for the entirety of Agents of SHIELD season 1 and Captain America: The Winter Soldier*

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1. Who or what is the Blue Alien?

In episode 14 (“T.A.H.I.T.I.”) Coulson discovers some shocking truths about his miraculous recovery from death at the hands of Loki in The Avengers. He should have died and he wanted to, but Fury made sure that he didn’t. Coulson learns that he was injected with the GH 325 serum, taken from an unidentified blue alien, and that his memories were altered to turn what was essentially torture, into a nice vacation at a “magical place.” We learn by the end of the season that Coulson was actually a part of this Avengers-last-resort-miracle-cure project but that he warned against it because of the negative it’ll-make-you-crazy side effects. This is why Fury assigned Agent May to keep an eye on Coulson throughout the first season.

From the markings on the alien body matching designs seen on aliens in Guardians of the Galaxy (mostly seen from the toy lines), along with a name drop from Chloe Bennet (Skye) herself (see here), we’re running under the safe assumption that the alien is a Kree, a species we’re going to meet in Guardians of the Galaxy when it hits theaters this August.

As for who this particular Kree could be, check out point #2. It was a head-scratcher that Coulson failed to ask Nick Fury in the finale about the alien, but again, we did learn earlier that pre-memory wipe, Coulson was a lead on that project so perhaps he knows. The audience however, still does not. In the end, that major plot point which may tie to the next Phase 2 film in the Marvel Cinematic Universe was swept under the rug… or at least an underground bunker’s worth of debris.

2. So, why is Agent Coulson special?

Nick Fury moved “Heaven and Earth” to keep Coulson alive, special treatment that according to S.H.I.E.L.D. officer Victoria Hand, (moment of silence, please) no ordinary officer in S.H.I.E.L.D. would receive. Drawing from comic stories for theories and hints from the writers, cast and executives behind the show, there was something epic and mysterious about Coulson’s return to life and the reason why he was brought back, but as we learned, he’s alive because simply because Nick Fury trusts him. That’s all, folks. He’s loyal, not alien or super-powered (read our old Coulson theories here). But it’s the how that’s more interesting…

The twist is that Coulson wasn’t special before, but he clearly is now. The end of the finale reveals that the memory wipe didn’t quite work as planned on Coulson and he’s begun to jot down alien text or markings on the wall, the same way crazy John Garrett (Bill Paxton) did after being injected with a variant of the GH 325 serum as well. We’ll explain why Skye doesn’t do this later  (see point #3) but Garrett was right in saying he and Coulson were cut from the same cloth. They are (or at least, were) connected. How?

What is this?

The blue Kree juice they took did something to them, whether that be transferring bits of memory or consciousness from the alien to them, or if the alien truly is Kree (and we think it is), it could have connected them to what Marvel Comics readers may know as the Kree Supreme Intelligence – a massive super-computer of sorts helping lead the Kree empire on their homeworld, built from the greatest minds of their people. Recall: Raina says to Ward  that Garrett is “connected now” after he goes full-on crazy in the finale.

All of that is way too over-the-top for the MCU as we currently know it, especially for casual ABC television viewers, but after Guardians of the Galaxy welcomes fans to the cosmos, then the series may begin taking advantage of its clearly alien plot threads. So, to go back to question #1, our theory about the blue alien (and possibly in effect, Coulson) being or becoming the character Geheneris HalaSon from Marvel Comics aka Captain Marvel (Mahr Vehl) could still be true and come true, so to speak. Coulson is special. More on that here.

3. Who or what is Skye?

One of the major blessings with Agents of S.H.I.E.L.D. that also happens to be its greatest problem is that the the creative team behind it is making a lot stuff up. They have to since its characters are all original and for the most part, are not from the comics. Even Agent Coulson was made up for Iron Man but has since found his way into an animated cartoon, a video game and even the books.

While Coulson is the lead of the series, the character the audience is meant to latch onto is Skye, the young outsider who had to earn her spot on the team from the get-go. She’s a hacker with a good heart who happens to have a mysterious and dark past. She also took a few bullets to the chest in episode 12 (“T.R.A.C.K.S.”) and nearly died until, like Coulson and Garrett, she had a dose of Kree GH 325 Koolaid and made a speedy recovery. For her recovery however, there were no negative side effects. She’s not crazy or dangerous, nor is she scribbling on the walls with a knife. Why?

Skye’s story and importance is one of the more frustratingly drawn out elements of the series, but it’s clearly part of a much larger plan. In episode 12 (“Seeds”) we learned that when Skye was a baby, many S.H.I.E.L.D. agents died trying to protect her and that she was classified by the organization as a 0-8-4 (an object of unknown origin). Skye’s not human and her no-consequence recovery from using the GH 425 had Fitz and Simmons secretly researching her seemingly normal DNA for a while. Combine this knowledge with the fact that Kree blood sustained her and there must be a connection.

The additional hint we learn in the first season’s final episodes is that Skye’s unidentified parents were the “monsters” responsible for the deaths of the agents in the Chinese village where she was recovered as a baby. Her parents are super-powered monsters, and her physiology works with Kree blood… Is she an Inhuman (see point #4 for more on this)? There are other alien possibilities (like the Majesdanians who left a child on Earth named Karolina Dean who joined the Runaways – a Marvel comic Joss Whedon wrote a few issues for) but the Kree blood might be the key hint, assuming of course, it is actually a Kree alien that we saw those many episodes ago.

Note: In chatting about Skye, Raina says to Ward that “her true nature will reveal itself” and described Skye as a monster. We’ll save the Ms. Marvel theories for another day.

4. Who or what is Raina?

Another made-up character for the show helping make it very difficult to surmise if this stuff is actually truly “connected,” Raina was introduced in episode 5 (Girl in the Flower Dress”) as an antagonist with an obsession for people with special gifts. It’s what made her loyal to the Clairvoyant, what drew her to China to capture Scorch (dude with fire powers), what had her interested in the Extremis virus and the Centipede program, and what has her involved in the happenings of the season’s last few episodes.

What is that thing?

As we learn in the final two episodes, she – like Skye – is not normal either. She says in episode 21 (“Ragtag”) she has something in common with Skye so if Skye is an Inhuman, Raina could be too. For a crash course on Inhumans, they’re people who share ancestry with early humans who were experimented on by the Kree millions of years ago. When they come of age, coming in contact with the Terrigen Mists (this may be a big plot point in future Marvel movies) mutates them and can grant them super powers or monstrous growths. It sounds strange but Marvel Studios boss Kevin Feige really wants to make an Inhumans movie and Marvel has been beefing up the Inhumans comics lately. That is all very intentional. Check out Marvel’s recent official guide to Inhumans and Terrigenesis to see for yourself here.

Fun fact and interesting connection: While writing for Marvel’s Runaways comics, Joss Whedon created a character named Klara Prast, who also sports the nicknames “Rose Red” and “Tower of Flower.” Her power is to control plants and in her mind, she “talks” to roses. Is Raina inspired from that character? It’s his character and his show, written by his brother and sister-in-law.

5. Who is Skye’s Father?

Skye’s father & Raina

At the end of the finale we see Raina meet up with Skye’s father, someone she knows but hasn’t seen in a long time. Was she exiled? We can’t see his face, but it appears he’s covered in blood. Is he an Inhuman, some other powered individual or another alien species? Is that a real character from the comics or another plot point made up for the show?

Skye’s dad has bloody hands

Does any of this truly “connect” to what we see in the mid-credits scene of Captain America: The Winter Soldier where we meet the super-powered “twins” known as Quicksilver and Scarlet Witch? Will these latest mysteries pay off in the films (a la Inhumans) or is this thread relegated to just the show?

6. What are the markings on the wall?

Now that we have the Inhumans and Coulson discussions out of the way, let’s focus on what exactly Coulson is carving into the wall at the end of the season. Ultimately, this is the biggest question and cliffhanger, serving as the post-credits button of the final episode. It’s the same pattern that Garrett began carving into a door with a nail earlier in the episode and has to do with the GH 325 serum they both took.

They, according to Raina, are “connected” to something that’s letting them see or understanding something humans shouldn’t see or understand. For that reason, we can assume it’s alien in nature. Is it a star map? Plans for Ultron? Alien text? Knowledge of the Inhumans or Terrigen Mists? Let’s hope this one is answered clearly and early in season 2.

7. What is Nick Fury doing now?

The finale finds a smart way to bring Nick Fury into the fold after he dropped his trench coat and eye patch at the end of Captain America: The Winter Soldier to go dark, working on his own while everyone believes him to be dead. The last we heard from him, he was headed to Europe to do something but we don’t know what that is. According to Samuel L. Jackson, his role in The Avengers: Age of Ultron is a “cameo” so he may not have much screen time. Is there any chance he shows up in Guardians of the Galaxy or in season 2 of the show?

Did he rescue Fitz and Simmons on his way to Europe or has he yet to go there?

8. Will Fitz recover?

Fitz makes the ultimate sacrifice for the person he loves most and we finally see him find a way to express his feelings for Simmons, but at the highest of costs. We know that Fitz survived the events of the season 1 finale but that his brain was deprived of oxygen for a long time. How severe is his brain damage and will we see the return of the quirky and lovable science duo in season 2 of Agents of S.H.I.E.L.D.?

9. What’s in the Toolbox?

The Toolbox

Nick Fury gives Phil Coulson the grand task of restarting S.H.I.E.L.D. from scratch, since he was always part of the “heart” of the organization – and for fans, the heart of the films. Coulson is now the Director of S.H.I.E.L.D. and Fury gave him a little black cube to help him begin. Isn’t that supposed to be Maria Hill’s job? Maybe she’s on assignment for Fury keeping an eye on Tony Stark, since she now works at his company.

Is the the box simply a hard drive with information S.H.I.E.L.D. database info? The location they travel to at the end of the episode is something Coulson got from the cube after all, but wasn’t all that info made public by Black Widow in Captain America 2 or is this other info for Fury’s eye(s) only?

Expect this magic mystery box to be the source of a lot of plot points for season 2. It could be cool or it could be the worst thing ever.

10. What will Coulson do next?

With Ward out and Agent Triplett filling his position as the team’s specialist, it’s all hands on deck (minus Fitz) going forward for Coulson. He and his team most re-form S.H.I.E.L.D. but with what resources? Look at what we saw in Captain America: The Winter Soldier in terms of equipment, vehicles and armies, and now look back at Coulson’s plane. That’s no S.H.I.E.L.D. which means we may have to see Coulson reuniting key SHIELD personnel and factions, reacquiring assets, etc., and maybe, just maybe, he’ll need the help of super-rich industrialist Tony Stark. Coulson still needs to meet up with The Avengers and tell them the really old good news that he’s still alive and has been for a while.

With ABC giving Agents of S.H.I.E.L.D. a second season, it’ll be on air leading up to and just after the theatrical release date of The Avengers: Age of Ultron next May. We’re very curious how Fury, Coulson and Hill will factor into the next team-up.

11. Is Koenig a Regular Now?

Agent Eric Koenig died at the hands of Grant Ward but actor Patton Oswalt is back in uniform handing out lanyards same as before. Same jokes, same rules, same dress code, same actor. We love Patton Oswalt but we were surprised to see him return at the very end of the series as Eric’s brother, Billy. Then again, Billy never refers to Eric as his brother and expresses no emotion over the apparent death of his sibling. Could Koenig be a line of Life Model Decoys used to maintain satellite S.H.I.E.L.D. bases around the globe for Fury?

Is this character going to have a more regular role in season 2? Or is he the one and only brother Eric mentioned and it’s simple as that?

12. What’s next for Graviton & gravitonium?

In episode 3 (“The Asset”) of Agents of S.H.I.E.L.D., we meet Canadian scientist Dr. Franklin Hall and see him kidnapped by businessman Ian Quinn. Hall was under the protection of S.H.I.E.L.D. but Quinn needed his help in building a gravity-altering machine (read: weapon of mass destruction) powered by gravitonium. The twist here is that Hall actually wanted to go there in order to activate the device and bring down the compound (and surrounding areas) they were in to bury the overly dangerous tech in the ocean at the cost of everyone who lives in that area, but Coulson saves the day (sort of) by dropping Hall into the machine where he’s absorbed into the gravitonium. Serving as a catalyst, the chain reaction stopped but at the same time, comic readers know that they just witnessed the origin of Graviton – a villain from the comics who can control gravity. We’ve yet to see him return.

As for the gravitonium, it plays into the final episodes as something Garrett promised to give Ian Quinn for his assistance. Raina wants it to go to Quinn too and in the finale we see them take it. He now has Graviton so expect a super-powered return in season 2.

13. The future of Grant Ward

Ex-Agent Ward, unable to speak by the end of the season 1 finale after a generous beat down from May, is now detained. We don’t know what authorities are responsible for his imprisonment but he’s alive and certainly not forgotten. If Ward returns in season 2, and we expect him to, how much of a role will he play?

We can safely say he’ll never be a part of Coulson’s “family” again, not after murdering so many soldiers and jeopardizing the lives of Fitz and Simmons, but we wouldn’t be surprised to see him cross paths with the team again. The finale made a point of emphasizing that Ward was never truly Hydra, nor did he care for their beliefs, but without his mentor (Garrett) to give him missions. Ward has no purpose or goals. He can only hope to redeem himself somehow, as impossible as that might be.

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Some fun tidbits:

  • Coulson is an Avenger according to Nick Fury
  • Best response to anything – Garrett saying “I am the key to the future of the universe” – works on so many levels for fans.

More: Marvel Plans Ahead All The Way To 2028

Captain America: The Winter Soldier is now in theaters, Guardians of the Galaxy opens August 1, 2014The Avengers: Age of Ultron on May 1, 2015, Ant-Man on July 17, 2015, Captain America 3 on May 6 2016, and unannounced films for July 8 2016 and May 5 2017.

Agents of S.H.I.E.L.D. returns this fall on ABC at its new time of 9pm on Tuesdays.

Follow Rob on Twitter @rob_keyes for your Marvel movie and TV news!