My overactive mind came up with an interesting theory about part of what HRG's real job is. (And how Nathan might not be Claire's father.) Possible plot bunny for someone better at writing plot-based fics than me. ::looks pointedly at
cornerofmadness and
kallie_kat::
We know that HRG studies people with abilities and that the Hatian is able to erase people's memories. It's also been hinted at that he knows Claude (or maybe that's just my imagination) and he probably knows what Meredith can do.
{Side note: Theory on Claude is that he used to work with HRG to help understand heroes and their abilities, but something wrong and he's been 'hiding' ever since.}
What if they've been studing "heroes" for decades? What if part of the research was a breeding program?
It wouldn't be difficult for them to take eggs and sperm from their captive heroes and use in vitro fertilization, then plant the fertilized eggs in surrogate (or the real) mothers.
So, even if Meredith and Nathan had an affair years ago, it's possible that Claire's father isn't Nathan because she was already impregnated. She just didn't know it. Or it was arranged for Meredith and Nathan to have sex so that when she discovered that she was pregnant she'd have a father in mind.