We have spent a ton of time now speculating over what the mysterious Theta Protocol is, and last night, the answer turned out to be way more straightforward than any of us guessed.
Most theories out there (including ours) figured it was Coulson messing around with building a team of Enhanced agents. While that still might be the case, it definitely isn’t what Theta Protocol is.
So what is Theta?
Theta Protocol was a covert undertaking led by Director Coulson, and overseen by Sam Koenig. While pretending to be recruiting more SHIELD agents around the world, Coulson had actually been traveling to a secret facility in the US where a Helicarrier was being housed. This wasn’t any random ship either, it was none other than Helicarrier No. 64, Fury’s personal command ship during the Battle of New York.
Post-fall of SHIELD, the Helicarrier had been mothballed. It was later recovered by Coulson, who set about bringing it back to operational status to be used in the event of some world-ending catastrophe.
Theta Protocol was ready to go as early as the Kree City event last season, but didn’t see action until Avengers: Age of Ultron this past weekend. During Ultron’s attack in Sokovia, Coulson and Nick Fury activated Theta Protocol, with Fury himself taking command of the ship to help evacuate civilians.
What happened to the Hellicarrier after this is never explicitly revealed, although Coulson’s later conversations with Robert Gonzales seem to imply that it’s still under Coulson’s command.