If you have not seen the latest episode of Agents of S.H.I.E.L.D. there will be spoilers.
During last nights episode of Agents of S.H.I.E.L.D. there were flashback scenes to an aircraft carrier during the Hydra uprising. Bobbi and Hartley rescue Mack, and they hook up with Gonzales. Bobbi says they have orders from Fury to sink the ship, and Gonzales says they cannot allow Hydra to get what it is carrying. What could they have that is so critical to keep out of Hydra's hands? They already have Loki's scepter, Thor took the Tesseract back to Asgard. Here are the points that I looked at followed by my guess as to what they were protecting.
1. "Real S.H.I.E.L.D. has some major funding coming from somewhere. Since Coulson is Fury's handpicked successor and has his toolbox, one would assume that he also has any hidden funds and accounts. But Gonzales and company are able to have troops, weapons, and operate an aircraft carrier. This is some major dough backing them.
2. When Bobbi was going to destroy the carrier, she was specifically going to take out the servers. While watching I assumed this was to cripple the ship so they could sink it. But then I began to think, what if the thing they had to protect from Hydra was on the servers, and that's why she had to destroy them?
3. Edward James Olmos has said that this arc will tie in to Age of Ultron. The synopsis for Age of Ultron states the Stark develops Ultron from an old security AI program.
O.k., if you haven't figured out where I'm going with this already, here is my theory. What if the AI that Tony later develops into Ultron is stored on the servers of that aircraft carrier? Tony Stark is funding the "real" S.H.I.E.L.D., and this connection is how he gains access to the A.I. All the pieces seem to fit.
What do you think? Does it make sense, or am I reaching?