The Marvel Cinematic Universe is completely interconnected though we haven't seen how all of it fits together yet. This allows for the fans to come up with a wealth of theories on how everything connects.
This article will contain spoilers for various parts of the MCU, so fair warning.
This particular theory involves a character that appeared in season one of Agent Carter. When the character first appears we know him as Ivchenko, but it's later revealed that his name is Doctor Fennhoff.
When he appeared in Agent Carter, he worked for a Soviet based organization called Leviathan, along with memorable psychopath Dottie Underwood. He tricked the SSR into trusting him. Shown to be adept at hypnotism, he hypnotized both Agent Yauch and Chief Dooley into doing things which ultimately got them killed.
At the end of the season, he's been imprisoned by the SSR. When we last see him, there's a metal muzzle over his face to prevent him from talking and hypnotizing anyone. He's led into his cell. Another man speaks to him from the shadows. It takes a few moments before we're allowed to see him, but it's revealed that his cell mate is none other than the infamous Doctor Zola.
My theory about Fennhoff had been formulating during the season, but I almost felt that it was confirmed by this meeting with Zola at the end of it.
Zola, as we all know, is responsible for the transformation of our favorite tragic hero, Bucky Barnes, into the Winter Soldier.
My theory on Fennhoff is that he was part of the early Winter Soldier Program. The degree to which he is able to manipulate people through hypnotism is frankly frightening. It only makes sense to me that he would have been recruited by Zola to do the same to Bucky.
When Fennhoff hypnotizes a person, he usually manipulates their memories, morals, or sense of loyalty. It's a very invasive, personal kind of hypnotism. It's also incredibly effective.
Bucky would have been seriously injured after his fall from the train when he lost his arm. However, we don't know if his memory was damaged at the time. Odds are, whatever was left of Bucky mentally at the time Fennhoff was recruited, Fennhoff manipulated it. Even if Bucky had few memories, it's likely his morals and loyalty were manipulated by Fennhoff. Bucky may have even been tricked into thinking he was killing for a good cause.
Fennhoff is likely the one that perfected the brainwashing technique used on Bucky and it was probably supplemented by torture.
Now this is just guesswork on my part. I know little of the comic book storylines, but I do know that the MCU doesn't always follow them. I did learn that one of Fennhoff's aliases, aside from Ivchenko, is Doctor Faustus, who is a villain in the comic book universe. Given the brief glimpses I saw of his history, it still makes sense to me that in the MCU, Fennhoff became involved with the Winter Soldier program.
I suppose only time will tell, though, as we get more insight into the Marvel Cinematic Universe.