Howard Stark spent 70 years searching the goddamn ocean for Steve. You want to know how many people he sent to look for me? They left my body bleeding in the snow, where HYDRA found me. But I guess it wouldn't have made a difference who found me, in the end.
Then Howard Stark recruited Zola -- the man who tortured me and took my memories -- as part of Operation Paperclip. He wasn't the only one like him. And no one should have been surprised when he resumed his work. SHIELD offered sanctuary to war criminals and funded technology that those criminals would eventually use to reprogram enemy combatants. Which was exactly what SHIELD designed it to do. MK Ultra was made to experiment with mind control. And Fury's vision for Project Insight was a hair's breadth from the project's realization.
SHIELD and HYDRA have always been the same. Since they began. Every mission you've accomplished has been under the ultimate direction of HYDRA. There is no hard and fast difference, no firm distinction between the two. They are one. They have always been one.