An update of my previous theory, that Lindenmann is the "Big Bad" of this season with
HRG underneith him:
(1.) He is obviously connected to people.
---(a.) He bribed/blackmailed Nathan.
---(b.) He was interested in Issac's painting.
---(c.) He is linked to Niki and D.L. in L.A.
---(d.) He has Hiro's katana.
(2.) This would explain HRG's "neutral good" morality. He may think he's doing good while being manipulated by Lindenmann.
(3.) I think it is unlikely that HRG actually is Lindenmann for the following reasons:
---(a.) Lindenmann lives in Vegas while HRG lives in Texas.
---(b.) Nathan was going to PROSECUTE Lindenmann. It is most likely that he has an idea what Lindenmann looks like, and Nathan also came in direct contact with HRG.
(3.) If HRG is Lindenmann's man on the inside, it would explain why the mysterious person he was on the phone with did not want Sylar to be killed.
(4.) His plans for Nathan:
---(a.) Nathan was the only one allowed to escape.
---(b.) As far as we know, nobody else has been able to use their powers around HRG and the Haitian.
---(c.) It would also explain why he is so willing to pay Nathan $4 Million dollars and why Nathan wins by a landslide.
(5.) There is no evidence thus far that HRG works for the government. In fact more and more the clues seem to indicate that he doesn't. In the web comics he claims to work for a government agency a couple of times but then he disavowels all knowledge when the new hero gets caught in the most recent comics. Other than wearing a suit and carrying around an air of superiority, HRG is just an average tool.
(6.) I find it highly unlikely that Lindenmann is the Petrelli's father.
---(a.) Nathan was going to prosecute Lindenmann, so I assume he knows what he looks like.
---(b.) There are references to "deals" between the two. Hard to have a deal if the two are the same.
(7.) I do think, however, that the Petrelli's father is a hero that will show up.
---(a.) Killed himself because of "delusions of grandier". (Although he may not actually be dead)
---(b.) Dealings with Lindenmann.
---(c.) The fact that 2 kids have powers.