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- While Hydra rarely gets to be AWESOME, it did utterly humiliate Norman Osbourne by absorbing the entirety of H.A.M.M.E.R. into its ranks. Effectively absorbing an entire branch of S.H.I.E.L.D. (the American one) to bolster itself.
- Madame Hydra didn't get one for seducing Wolverine; that's easy enough when you're a sexy villainess, but using it as political leverage to take over a country is another matter.
- Baron Strucker blowing up an entire base of Hydra agents to annihilate the Skrull infiltration of his organization. Possibly a little excessive, but still awesome nonetheless.
- While a Pyrrhic Victory for all, Hydra managed to defeat the Howling Commandos PMC in a straight-up military conflict. It was the one time Nick Fury miscalculated.
- Subverted with Hydra having been in control of S.H.I.E.L.D. all along in Secret Warriors. Nick Fury knew all along.
- The sheer longevity of the organization revealed in Secret Warriors. Baron Strucker's branch is just one of them and it's been kicking around since Ancient Egypt.
- Subverted by Hank Pym rescuing the President of the United States from a massive Hydra attack. Not only was it not the real Hank Pym but the Hydra agents were probably suicidal Skrull agents.
- Nick Fury taking down the entirety of Hydra Island and saving the world from the Death Spore virus.
- Wolverine's revenge for his mind-control is to try and kill every Hydra goon on the planet. He almost succeeds.
- Nick Fury gets his greatest one at the end of Secret Warriors. Destroying Baron Strucker completely by revealing how much a fool he'd been played before executing him.
Marvel Cinematic Universe
- In Captain America: The Winter Soldier we find out Hydra used Operation Paperclip and caused the entire Cold War as well as numerous other tension-growing actions. They used S.H.I.E.L.D. to rebuild themselves and even manage to kill Tony Stark's dad. In the end, they came closer to victory than any other villains in the MCU at that point, within seconds of completing their plan. In short, they truly showed their genius (and evil).
- This carries over to Agents of S.H.I.E.L.D. where we discover the Clairvoyant who has been running rings around the heroes for some time is actually Garrett, their S.H.I.E.L.D. contact and secret member of Hydra.