After the reveal that HYDRA has infiltrated S.H.I.E.L.D. throughout the last 70 years, many past exploites of S.H.I.E.L.D. in MCU take on a new light and leaves lots of room for speculation for the future.
Tesseract research
In
The Avengers, it is shown that S.H.I.E.L.D. had been researching the Tesseract to make weapons, much like HYDRA had in the first Captain America movie, even going as far as collecting WW2 HYDRA weapons. However what if there was more to the research, (which itself is potentionally bad enough) as no one seems to question why the device that S.H.I.E.L.D. built seems to make a better portal platform than any form of energy collection. They knew the device created a doorway to another part of the universe but maybe they didnt expect the bring Loki through it maybe they were trying to bring leader back through, the Red Skull.
Slingshot
In the TV show, it was revealed that when S.H.I.E.L.D. find technologies too degerous to keep they would be disposed at the Slingshot facility by being shot into the sun. However, it now seems more likely that this was a ploy by HYDRA to smuggle out dangerous tech to their own research facilities around the world, and this might explain how Baron Von Strucker obtained Loki's staff.
US government
What alot of people are forgetting is that not only S.H.I.E.L.D. that was infiltrated but also positions within the US Government and who knows where else. Senertor Stern's reveal adds more layers to Iron Man 2 plot and most likely explain how S.H.I.E.L.D. got into the position of having a seemingly unending budget. What if high levels of the military have also been got at by HYDRA, I some how dont see Emil Blonsky being held under lock and key much longer.
Anyway thats a few of the little thoughts that ran through my head today, but what do you guys think, am I being paranoid? Sound of below.
Hail HYDRA!