I've only seen the first four episodes, but if I understand correctly the Prisoner in the first series was some kind of secret agent, where this Prisoner was an IT guy for a company that gathers information on people.
He found out too much information and "resigned", so his former employers captured him and whisked him off to the Villiage, where they are trying to find out what he knows and I'm guessing what he told to who before he resigned.
Anyway, that's my take on the show so far.
That is my theory, which is mine, by A. Elk.