Before Hydra was in the Captain America movie (as a more international market safe Nazi pseudonym), it was the ultimate SHIELD enemy in the comics; in G.I. Joe terms, Hydra is Cobra.
As it happens, a number of the G. I. Joe
characters were based on a failed pitch Larry Hama had made for a team called Fury Force, which would've been "a group of specialized soldiers who worked for SHIELD" -- a similar concept to this show, albeit more military. However, despite this, Cobra was not based on HYDRA, even though it would be natural to expect that they were. (Source
Although, I must admit that when the enemy agents came in to abduct "Scorch" in last night's episode, my first thought was that their flame-resistant suits looked like the AIM bee-keeper outfits.
Hmm, do you suppose that could've been an intentional nod? Anyway, as I've mentioned before, in the comics AIM was originally HYDRA's special-weapons research division. My expectation all along has been that the archenemy would be AIM and the team would discover their link to HYDRA.
I'm wondering who the man in prison was. I can't help but suspect that his line "You know I'm not going to do the talking" is a clue of some sort.