How do the shocking revelations of Captain America: The Winter Solider and Agents of S.H.I.E.L.D. change what we all thought we knew about the MCU?
In retrospect, The Avengers Initiative almost seems like the early stages of Project: Insight, doesn't it. While I think it's open to speculation whether or not Fury's operation was entirely on the books, it's obvious that the World Security Council, which we know was compromised, knew about The Avengers Initiative and it's also very obvious that at least a few other members of S.H.I.E.L.D. knew about it as well, making the whole process subject to doubt. With that in mind, it shines a new light on one of every fanboy's favorite scenes from Iron Man 2:
All this time these maps just seemed like nerdy Easter Eggs giving us the locations of some of Marvel's heroes. We know, from Iron Man 2 director Jon Favreau, that 2 of the spots on the map are connected to the events of Captain America: The First Avenger, one to Thor and that the spot in Africa is a reference to the Black Panther. With the revelation that Arnim Zola has been a living A.I. for quite some time now, this map begins to take on another level of meaning. We know this map was Fury's way of keeping his eye on some special people, but how did these people come to his attention? At this point, we can't rule out Zola's algorithm, which was the mathematical basis for Project: Insight, having something to do with identifying these points on the map.
Phase 2 Weapons in The Avengers
When Nick Fury revealed to the Avengers that S.H.I.E.L.D. had been using the Tesseract to develop weapons, it seemed a very shady move on his/their part. With the added information that those weapons were actually being developed by a S.H.I.E.L.D. that had been deeply infiltrated by HYDRA, who had originally used the Tesseract to make weapons in the past, it certainly adds another dimension of bedevilment.
The World Security Council
With the revelation that Alexander Pierce was a long-time HYDRA flunky was a powerful member of the World Security Council, we have to question every decision that was made by the group, most notably the launching of the nuclear weapon into Manhattan. It's pertinent to wonder, in light of Pierce's influence over the council, if the nuke was meant to take out the Avengers as much as the aliens. And remember, the Council certainly wasn't happy that Fury let Loki, who had learned how to use the Tesseract, and the Tesseract itself get away from them. HYDRA would have loved to have entered into an arrangement with the God of Mischief.
Anything That Involved Jasper Sitwell
Remember he was present when a S.H.I.E.L.D. team, led by Agent Coulson, boxed up the research of Dr. Selvig and Jane Foster. One really has to wonder what HYDRA might do with the work on inter-dimensional portals. He also circumvented his orders in Item 47 by keeping the Benny and Clare alive and, as of now, we have no idea what became of the pair. And, in what was almost certainly not a coincidence, Sitwell was stationed at the S.H.I.E.L.D. base The Hub alongside non-HYDRA agent Victoria Hand. Also, in hindsight, it seems Sitwell showed his hand a little when he queried Agent Coulson on his time in Tahiti. As part of his cover, Sitwell was sent to the Lemurian Star to guard vital information on Project: Insight. When viewed as a whole in hindsight, Sitwell's career with S.H.I.E.L.D. looks very suspect.
No wonder he was leading the charge to have Stark's Iron Man armor handed over to him. Senator Stern's main motivation was always to reign in Tony Stark and, more importantly, the Iron Man armor. While he put up pretenses that it was because Stark operated outside the influence of the U.S. Government, it becomes clear in hindsight that it was because Stark operated outside the influence of HYDRA. After the U.S. Government got its hands on the War Machine armor, it wasn't long before A.I.M., a comic book branch of HYDRA, used the armor as part of its plan to kidnap President Ellis.
Speaking of A.I.M.
Just how connected are A.I.M. and HYDRA. While A.I.M. was once a branch of HYDRA that worked on the creation of advanced weapons, they eventually became completely separate entities and even went to war from time to time. It's easy to speculate they were connected during the events of Iron Man 3, which can be looked at as just one more effort to eliminate Tony Stark, but what about in the aftermath. With Aldrich Killian likely dead, A.I.M. will have to regroup, but we certainly haven't seen the last of them. A.I.M.'s main work seemed to center around Extremis, but they were certainly working on many more projects. The questions are how many of them had ties to HYDRA and when will we see A.I.M. again? The picture above may remind you that they had a much larger presence in Iron Man 3 before being cut out in the editing process.
Was Obadiah Stane a member of HYDRA? Upon the death of Howard Stark, Stane assumed control of Stark Industires. Since HYDRA had Stark killed, it's not wrong to question if they got to Stane either before or after Howard's death and used him to help control the war business. It's safe to assume Zola's algorithm would have picked up on Tony Stark as a threat LONG before he became Iron Man and wonder if there's any connection to HYDRA and Stane's attempt on Stark's life that was responsible for him becoming Iron Man. Ironic, I'd say so!
Baron von Strucker
At this time, he seems to be the head of HYDRA. One has to question how long he's been in charge and then how many events in the MCU has he controlled. We know his next move, the unveiling of the Maximoff twins, but we don't know which moves he made before that. That's something that would make a nice One-Shot, the real history of the MCU starring Baron von Strucker now that we know HYDRA has had its hands in everything. Given that they have access to Loki's scepter, it's probably ok to assume they have had their hands on a few other things that they shouldn't have that may cause some big trouble for the Avengers.
The Avengers: Who Can We Trust?
We know Captain America is as safe as it gets. Iron Man too. I can't imagine any way that Thor would be anywhere but on the side of justice and Bruce Banner would never be involved in subterfuge. Hawkeye has had a murky past, but there's no past murkier than that of the Black Widow and we have only just barely seen anyone have any sort of trust issues with her. As a comic book character, the Black Widow spent the majority of her early career with no clear allegiances and was notoriously a double/triple-agent. In the MCU, we've really seen nothing of that and maybe it's time. I'm not saying she'll end up being a villain, because when it's all said and done, she isn't. I am saying it might be time to start instilling some doubt into the audience, maybe even have her working with/for HYDRA for a while. While it's easy to dismiss this as baseless speculation, keep in mind it would mean ignoring a huge part of who the character actually is. Instead of ignoring it maybe, after all this time trusting her innately, it's just the right time to bring that development into play. Remember, she's more loyal to Fury than she is to anybody else in the MCU making it possible he may send her underground sometime soon.
A lot to process for sure, and this was by no means all-inclusive. The revelations are not done, by any means. The next five episodes of Agents of S.H.I.E.L.D. will likely continue to add more and future MCU installments will certainly address the past in bits and pieces. One thing I think we can be sure of is that, despite the best efforts of HYDRA, a team of heroes has been assembled with the power to change, protect and avenge the world and it won't be long before the Avengers come face-to-face with HYDRA.