I tend to believe the Haitian's work for the comapny was just a front. I forgot about his work with Angela Petrelli from last season, but could that maybe put Angela and HRG as a tandem? I got the distinct impression that the Haitian wiped Peter's memory and locked in the cargo container as a way to protect him. That serves both Angela and HRG. HRG would want Peter out of the way and neutralized -- his M.O. seems to be the fewer people with powers there are, the more safe his family (i.e. Claire) will be. Angela would just want to know her son is safe. I also sense the Haitian's true allegiance is to others with powers. He tends to go out of his way to protect them when he is supposed to be either wiping their memories or killing them.
As for Adam, what an enigma he is turning out to be. A lover scorned makes a classic back story for a baddie, but he looks like anything but at the moment. Given that almost every theory I've posited on this show has been wrong, take this with a grain of salt, but here is something to think about. In talking to Nathan, Bob portrayed Adam as the bad guy. He also said Linderman was Adam's disciple. Could Linderman, with the backing of the 12 (and hence The Company) have revolted against Adam and unjustifiably locked him away? Remember Adam was in there for 30 years. As I said eariler, that is reason enough to start killing the remaining 12 off.

