Theta Protocol was a S.H.I.E.L.D. protocol led by Director Phil Coulson. It was an operation located at the Theta Protocol Facility to secretly repair Helicarrier No. 64 so that in case of a grave world emergency, it could be recommissioned.
Theta Protocol was a project created after the collapse of S.H.I.E.L.D., when Nick Fury and Director Phil Coulson learned that Helicarrier No. 64, albeit damaged, survived the war and HYDRA's attempt to capture it. The idea was to secretly repair Helicarrier No. 64 so that it could be used in case of a world-threatening emergency. The Helicarrier was brought to the Theta Protocol Facility, run by Sam Koenig, where repair work began.
Coulson informed Melinda May that he was heading to London to recruit more former S.H.I.E.L.D. agents into their organization, but in reality, he met with Sam Koenig in the United States to discuss Theta Protocol. Koenig handed Coulson his new S.H.I.E.L.D. Lanyard before overseeing the progress of Helicarrier No. 64's repair work.
As Coulson's agents prepared for the Battle for the Kree City, Coulson told Sam Koenig to report back to the Playground, stating that if things went south he would need Sam and his brother to enact the Theta Protocol, much to Koenig's dismay.
According to Agents May and Jemma Simmons, Coulson did not tell them about the Protocol. The separate faction of S.H.I.E.L.D. led by Robert Gonzales saw this as prime example of Coulson keeping dangerous secrets, which they saw as the reason for S.H.I.E.L.D.'s original collapse.
After being contacted by Maria Hill and briefing her on the whereabouts of the Scepter, Phil Coulson was asked if he was ready to activate Theta Protocol. He affirmed so, claiming it was time to bring in the Avengers.
Theta Protocol was activated by Phil Coulson and Nick Fury, recommissioning Helicarrier No. 64 to support the Avengers in the battle against Ultron in Sokovia. The Helicarrier was tasked with evacuating the civilians remaining on the flying city landmass, using incorporated evacuation pods to do so. The Helicarrier also aided War Machine in preventing rogue Ultron Sentries from escaping the battle, shooting them down.
Revealing the Truth
Phil Coulson revealed to Robert Gonzales and his board the true meaning of Theta Protocol. Gonzales was relieved to hear that Theta Protocol was only a Helicarrier. After that, Gonzales agreed to Coulson's offer to unite the two factions of S.H.I.E.L.D. into one strong organization.
In chronological order:
- Agents of S.H.I.E.L.D.
- Avengers: Age of Ultron
- Captain Marvel Prelude (concurrent events)
- Agents of S.H.I.E.L.D.