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Hydra is a criminal organization dedicated to world dominance through terrorism and various activities including assassination and use of extreme stealth through advanced technology. Its activities and age resulted in a fascist New World Order as its extent of operation is also international / worldwide, the organization using counter-espionage tactics and luring S.H.I.E.L.D away most of the time as they oftenly escape Nick Fury's observation, not to mention C.I.A or F.B.I.

HYDRA symbol as a giant squid reaching its tentacles around the world and control

One of its oldest founders is thought to be Johann Schmidt ( Red Skull) who funded the organization somewhere during WWII, however, its true leaders are still hidden or unknown. Before The Mutant Registration Act, HYDRA stalked information about The Super-Soldier Program, and though it proved to be a failure over time, its leaders moved their interest in collaborating with the military scientist, William Stryker, to use mutants to fullfil their own deeds and evil plans. 

The Hidden Agenda & Aftermath ( X2: United & X-Men: The Official Game)[]

Before building a prototype Cerebro to eliminate all mutants, Stryker used his resources to complete Project: Wideawake using HYDRA technology, though the latter tought that eliminating them instantly would be more convenient and canceled the project after finishing Master Mold, leaving the project in ruins. After Stryker dies, Kenuichio Harada becomes the new head of HYDRA and accidentally activates Master Mold after sending his agents to investigate the underground base left in ruins. The organizations' second in command is Yuriko Oyama after seemingly survived the adamantium infusion made by Wolverine.  Before Silver Samurai is defeated, most of the HYDRA agents are defeated by Wolverine, thus leaving the organization vulnerable for a time.

Before Stryker's death and invading the X-Mansion, HYDRA agents used the colonel's resources and military access as the latter provided them normal machine guns, equipment and fighting gear, so they won't get exposed after Stryker finishes his plans.