Agents of SHIELD: What is the Theta Protocol?

On tonight’s episode of Agents of SHIELD, we find out that Coulson has been keeping some big secrets from his own team.

According to Robert Gonzales’s “real SHIELD,” Coulson has been investing heavily into something called the “Theta Protocol.” This wasn’t the first mention of the Protocol though, it was planted way back in December during the mid-season finale. During that episode, Coulson tells Agent Koenig to activate the Protocol if things go bad during the Kree city mission. It doesn’t come to that though, so we never get to find out what it would have done.

Here’s what we do know for sure:

• Coulson is funneling a ridiculous amount of money into the Theta Protocol project, at least as much as the rest of SHIELD’s budget combined.
• He’s purchased a hundred bunk beds, which leads Mack to theorize that it’s for a new base.
• He’s been taking secret meetings around the world, including Dr. Andrew Garner, Melinda May’s ex-husband, and a former SHIELD psychologist.
• Deathlok technology is being leveraged somehow, and Coulson is directly in touch with Deathlok himself.
• Agent Koenig was told to activate the Theta Protocol if things went bad during the Kree city mission. That implies that whatever it is, it was at least somewhat operational months before the “real SHIELD” takeover attempt.

Gonzalez’s SHIELD faction believes Coulson’s goal is to create a team of superpowered individuals for some currently unknown reason, and is currently recruiting, bringing on people like Dr. Garner (who has experience dealing with enhanced individuals), and weaponized super-agent Deathlok.

If that’s the case, it’s no wonder why he might want to keep it a secret from the rest of his organization. The team has faced nothing but trouble during their run-ins with powered individuals, from “Crusher” Creel to Cal’s team of villains; and this episode revealed just how much May’s life was affected by a confrontation with an Inhuman seven years earlier.

If this is the case, and Coulson is building a team of superheroes under the SHIELD banner, we have a few ideas on how the Theta Protocol might play out.

Secret Warriors

I’ve been seeing this theory floating about social media the most, and it makes sense. Secret Warriors followed a covert ops team led by Nick Fury, and included none other than Daisy Johnson as a founding member and team leader. While there’s no big “ah ha!” moment here linking it to what’s happening in Agents of SHIELD, there are a ton of little connections that really start to add up.

The team was formed in the aftermath of the Skrull invasion of Earth, but really came to prominence during the Dark Reign storyline. During that arc, Nick Fury reveals that HYDRA had been secretely infiltrating SHIELD for years, and soon after, SHIELD was officially disbanded by the US government. In the fallout of that, the Fury tasked his team with preventing HYDRA from acquiring former SHIELD assets and bases. That’s already starting to sound very familiar.

Additionally, a point of conflict in the series was that Fury was leaving the team in the dark about many things (just like Coulson is now), and was even overseeing two separate teams that he was keeping a secret from the main one. Replace Fury with Coulson, and Secret Warriors seems to make a really smooth transition into the Marvel Cinematic Universe (the storyline also featured both Alexander Pierce and John Garrett as good guys, in case you need a few more useless but interesting MCU connections).

The only thing that would be tough to buy is the idea of Skye being able to lead a team of her own. On the other hand, Agents of SHIELD has clearly been positioning her as a lead for some time now, and with both a mysterious spin-off and an Inhumans movie in the works, she’s poised to play a huge role in the events to come.

Secret Avengers

Another possibility is the MCU’s take on Secret Avengers (there sure are a lot of secrets). This team was formed in the aftermath of Dark Reign, a storyline where Norman Osborn disbanded SHIELD and formed his own version of the organization. In response, Steve Rogers (aka Captain America) creates the Secret Avengers, a team of superheroes that engages in black-ops, off-the-books missions.

However, this isn’t the team we’re talking about. We actually want to take a look at the second incarnation of the Secret Avengers. This version of the team was formed by SHIELD itself, with Nick Fury, Maria Hill, and Phil Coulson among its leadership. Obviously all three of those names are no strangers to Agents of SHIELD.

The new Secret Avengers continued to take on the role of black-ops operatives, and embarked on missions such as taking down terrorist cells. The idea of a darker, gritter version of Agents of SHIELD seems like it could be a cool direction for a potential spin-off series, especially if its membership is exclusively superpowered individuals like Skye and Deathlok.

To link things even further to the current universe, the Secret Avengers membership also included Black Widow, Hawkeye, and Mockingbird (all established characters in the MCU), and operated during the era in which Daisy Johnson herself was the director of SHIELD.

Something Age of Ultron Related

Another possibility is something completely separate from the comics. The promo for next week’s episode was really pushing the Age of Ultron link, and while that might have just been misleading marketing, we do have two more episodes before the movie comes out. That’s plenty of time to set up and resolve some tie-ins if Marvel wants to, and if it’s anything like the Winter Soldier situation, then the episode immediately following opening weekend will feature the aftermath of the movie’s events.

While I doubt SHIELD is directly involved in anything Ultron related, it’s very possible that the situation with the Maximoff twins could factor in. We know that they’re the result of HYDRA experiments, so it’s not completely unrealistic to think that Coulson might be pursuing his own means of creating superhuman agents.

Centipede (Again)

It’s worth mentioning that the machine used in the show’s first season to unlock Coulson’s memories was called the Theta Brain-Wave Frequency Machine. While that’s nowhere near conclusive, it is kind of weird that Agents of SHIELD would be throwing around the term “Theta” again so soon.

Could the Theta Protocol be some way to create superpowered individuals, possibly through the use of former Centipede tech?

The Way Out of Left Field Theory

Is this likely? Definitaly not, so please don’t yell at me in the comments… but they do need an origin for Captain Marvel…

We know the eventual movie will follow the Carol Danvers version of the character, and in the comics, her background is in the US military. I don’t think it would be that crazy to think that the movie version came out of a SHIELD program instead, one that maybe even gave her enhanced abilities.

Again, very unlikely; but we know for a fact that Joss Whedon was pushing for Carol Danvers to cameo in Age of Ultron (with her superpowers and everything), and even went as far as to shoot the scene before the character was ultimately cut. That potentially means that Marvel already has a plan in place for the character, and as we know, everything is connected…