Hydra starts off as a special unit in the Nazi regime, tasked with investigating supernatural phenomenon and developing experimental weapons. When the Nazis lost the war, Hydra went underground, secretly recruiting members and infiltrating various governments and security organizations like SHIELD, with the long term goal of taking over the world. We don't know about other organizations but they were particularly good at infiltrating SHIELD, compromising a large segment of their agents. In Winter Soldier they were finally ready to make their move, attempting to seize control of the new helicarriers, whose weapons and advanced data systems would have allowed them to eliminate opposition.
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