Hydra is a powerful and far-reaching international terrorist organization formed by members of the inner circle of the Nazi regime in World War 2. It was originally conceived of by the Red Skull, but survived thanks to stolen Nazi wealth and sponsorship by rogue states, to become the powerful international criminal organization that was in large part responsible for the formation of SHIELD.
It has had numerous leaders through the years, with occasional internal strife and the spinoff of different factions (including AIM and the Shadow Empire). It is currently led by Baron Strucker, an old enemy of Nick Fury’s whose lifespan has been radically extended by Hydra super-science handed down form the Nazis.
As well as its own shock troops and advanced technology, Hydra regularly employs super-powered mercenaries and killers-for-hire, though they are notably anti-mutant (a holdover of Stucker’s Nazi philosophy).
Hydra was directly involved in the assault on Stark Tower, where they launched the armored super-merc known as the Titanium Man from a small stealth attack submersible before fleeing the scene. It appears they are working in concert with AIM and The Hand, a very unusual situation that the heroes are investigating. (Assembly Required #1-2)