assetandmission:

We know that HYDRA couldn’t completely erase Steve from Bucky’s memory… but maybe they knew that, and manipulated it to their advantage. It’s eerie how much a young Robert Redford resembles Steve Rogers during the 1940s:

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Maybe HYDRA chose Pierce to be Bucky’s handler based on his striking resemblance to Captain America. Perhaps he rose through the ranks because of how well he could control Bucky, without using extreme violence. He would have been the perfect brainwashing tool.

So how many times did Pierce take Bucky’s love for Steve and use it against him? Is that partially how HYDRA made Bucky so complaisant, so willing to take orders from Pierce? 

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A young Alexander Pierce would just have to smile at Bucky while spewing lines about Saving the World, and The Greater Good, and Bucky would have listened. It would have sounded so familiar to him, manipulating the part of his brain that would follow Steve Rogers anywhere.

The manipulation is especially noticeable in the vault scene. Seeing Steve on the bridge confused Bucky, but Pierce brings him back to focus by lecturing him about doing his part to shape the century. Bucky looks abashed, until Pierce says: “[if we don’t do our parts]…HYDRA can’t give the world the freedom it deserves”. At those words, Bucky really looks at Pierce, actually considers him for the first time:

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He has a bite to his voice as he replies “But I knew him” – so different from his submissive behaviour seconds before – because now that he remembers Steve, he doesn’t implicitly trust Pierce. Bucky looks resentful, like he’s seeing the manipulation for what it is, though he doesn’t understand why.

Even as his memories return, Bucky could be wary and nervous of Steve, confused by HYDRA’s manipulations. It could explain why he’s running from Steve in Civil War.