In “Winter Soldier”, we see Captain America working alongside SHIELD agents on covert missions around the world. It doesn’t really seem like a big deal at first glance, but if you think about it, it’s kind of irrelevant. After being unfrozen, Steve Rogers was quickly thrust into the intergalactic skirmish chronicled in “The Avengers”, during which he and the other heroes discovered that SHIELD Director Nick Fury had been manipulating the team from the start, hiding information about their plans to weaponize the Tesseract (yes, HYDRA was still secretly infiltrating SHIELD at the time, why you ask). Steve legitimately saw this as a continuation of Red Skull’s work and opposed it, even though nothing really seemed to change.
Steve would spend the next few years working with SHIELD under Fury, any animosity seemingly forgotten – but what’s worse, he did so even after learning that Fury was once again developing secret weapons through Project Insight. When Fury tells Cap to “get on the schedule”, Steve tells him not to hold his breath and, as expected, Project Insight is hijacked by HYDRA to eliminate all of their enemies (including the President of the United States). Luckily Captain America is able to save the day, but it all begs the question: why was he willing to work with them for so long in the first place, especially when he knew Fury used to lie to him on his way back. when they first met?