The Hydra was a mythical beast that was slain by Hercules. It had many heads (usually 3 but sometimes up to 12), if you cut one off, another (or sometimes two depending on the version) would grow back in its place. A hydra organisation is one that doesn't have a leader per se, it operates as cells which follow the same set of rules. So effectively, if a 'leader' is killed, the organisation goes on without any problems because it has loads of others operating at the same level. It's one of the main reasons why a 'war on terror' is the stupidest idea this planet has ever had and it's a war that can't be won.