Is it possible that the writers have thrown us another twist?

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I think this is the right line of thinking, but like "5 Years in the Future" from season 1, it is probably the doing of Sylar after having taken the powers from Alejandro and Maya. Now, someone in the Company wants to keep Sylar (aka Gabriel Grey) alive. I think it is Bob...who I also believe is linked to Sylar in a strange way...perhaps his father. Who knows, maybe Elle is also Bob's daughter and Sylar's 1/2 sister. They are tracking Peter down because they know he is the only one who can stop Sylar if Sylar continues to acquire different powers. It would also explain why Bob is so hell bent on developing a strain of the Shanti virus which just causes ability loss rather than death. It would be a way to save his son. Any thoughts?

Maybe it's both. Maya's power could have unpredicted results from the Shanti Virus.
(Like the Legacy Virus and Mutant DNA)

I think if he wanted to save his son he should have been more present in his life before he murdered lots of people in horrible ways!

Nice thinking, though.