In Avengers: Age of Ultron, it was revealed that "theta protocol" was a secret helicarrier that Fury and Coulson had built.
Ultron created a giant anti-gravity generator and planned on using it to cause a large city in Sorkovia to float into the sky and then drop it down to Earth like a meteor thereby causing a global extinction event. The Avengers wanted to stop Ultron by destroying the city before it could reach Earth, but they had no way of evacuating any of the city's people which is when Fury enacted "theta protocol" and arrived with his helicarrier. S.H.I.E.L.D. deployed lifeboat hovercrafts to the city and began evacuating people onto the helicarrier. Iron Man and War Machine protected the helicarrier from Ultron while the other Avengers help gets people onto the hovercrafts.
In the Show Edit
Throughout Season 2 of the show, "theta protocol" was hinted at, but wasn't fully explained until Avengers: Age of Ultron.
After Fury appointed Coulson as the new director, Coulson began traveling around the world on solo missions citing them as recruitment missions to find new S.H.I.E.L.D. agents. However, it's later revealed that Coulson lied to the others and was really working on "theta protocol" with Fury.
In "Melinda," Gonzales and Weaver explain to May how Coulson has been moving agents and resources all over the world, but they don't know what for and all of these actions are linked to something called "theta protocol." Their group believes that "theta protocol" is another secret base, one made specifically for powered people, and that Coulson is attempting to create some kind of super-powered army.
After Ultron is defeated, Coulson tells Gonzales and the others the whole truth about "theta protocol."