Also, it just never made sense to me that Chandra went to all this effort to keep Shanti's death a secret from Mohinder, but felt completely free to blab about it to Mr. Bennet in "Six Months Ago."
Which makes me think that either a) Chandra had just as many son issues as Mohinder had daddy ones, or b) his heart wasn't as cold as all that. I see Chandra as honestly caring for Mohinder, in however abstract or disconnected a sense, but unwilling/unable to let him get close, perhaps out of some perverse desire to protect him or atone for something. Mohinder, no matter how innocent he was of Shanti's demise, was conceived primarily as a cure for her disease, and so first and foremost, before he could walk or talk, he was a failure. I don't know if Chandra was aware he saw Mohinder like this, but I do think he knew he had some serious flaws as a father and, while accepting that while he would never be close to his son, he could at least protect him; which is why he distanced Mohinder from the research and never let him know the very reason he exists. I think Chandra was coldly analytical and so emotionally crippled he was unable (or afraid) to express what he felt in rational terms, but he was also a
feeling individual. This is why he wouldn't tell Mohinder about Shanti and the virus, even though Mohinder could arguably be as or more useful than the Company in utilizing that information, but would tell Bennet; because Bennet would not be hurt by that information. Clumsy though it was, Chandra was honestly trying to do a good thing for the son he couldn't connect with.
Although it's a little interesting to me that anything could have a disillusioning effect on Chandra... he seemed to live up to his "heart of stone" mantra pretty well.
Chandra talked about his heart of stone and he's definitely been shown to be a very facts-oriented, logical person, in keeping with the role of scientist, but he must also have been deeply passionate, and considering the nature of his research, he would have had to have some very idealistic part of him, expressed through science. Remember, he thought of "evolution" and took the leap to "superpowers" when
no one else did. I think in part this was due to Shanti (most likely) having an obvious ability, but at the same time, he went to a fantastic place and held strong to it. He wrote a book and moved across the world tracking these people down. Scientist or not, heart of stone or not, he didn't strictly look at disparate facts, he also imagined what those facts would amount to (like Gabriel and his watches, he very carefully took a bunch of insignificant parts and built something amazing), and he must have foreseen that his discoveries would change the world as we know it. Forget disillusionment, when Patient Zero crashed and burned and, for all intents and purposes, took the entire future down with him, Chandra must have been
devastated. He could have taken two roads from that point, the first of which being to get back on his feet, contact someone else, and start again, but since he choose Door Number Two (never physically seek out a super again), I think something must have been irrevocably broken inside him by his failure - remember, the second time he's failed with a Hero, the first being his own daughter. This is why Chandra turning dark is such a fascinating, and almost inevitable, concept for me.
As an aside, "Shanti" means "hope."
They just didn't get the List, because it was in super-sekrit code. Which begs the question, if Sylar could get his hands on it so easily, why couldn't the OWI?
They did have the list, I think. After all, they told Mohinder they didn't need it, that it was the genetics they were interested in. They had the old list; what they were after was a new and improved way to find Heroes.
contacted only Claire that we know of
If he contacted Claire, I missed it. She did get her hands on his book, but that was courtesy of Zach, not Chandra himself.
Did they have him killed?
I love this theory, especially since it was never really confirmed that Sylar did the deed. If this is the case, it would go a way towards a) redeeming Sylar, b) casting light on the Company and Chandra's interactions with them, and c) screwing Mohinder over
again. It would be the second time that poor boy was duped by someone who had a hand in his father's death.
Was the copy Mohinder found just a back-up copy, and a perfectly good paper one was among the stuff they took?
This is probable, and brings to me another interesting point: the Company knew about Chandra's death before Mohinder did. Not only that, but they knew the location of at least two of his apartments (he may have had other hidey-holes that he kept secret and were never found). They were already aware of his existence, his research, and his past, so either they were keeping tabs on him or he was actively working with them; either way, since they had the list and Bennet knew details about Shanti, one or the other had to have made contact.