Well, a bunch of stuff bothered me about this one. It was enjoyable on some levels, but I just didn't buy some elements.
Like the reasoning for the Captain and one other person to be sent back. Isn't that the whole purpose of the organization that Daniels belongs to? To take care of those things and not contaminate people from the past? The excuse given was that they didn't have time for the paperwork or something. Was there less work to send two non-affiliated people back in time, thus contaminating them? What sense does that make?
Plus, the plan to make the virus back then and then transport it forward to the current time to use it. Why? Why not just finish off the humans right there in 2004? Clearly they were thinking of limiting them. Not only that, 2004 would be much better time to do it, since there weren't any humans known to exist off planet. Problem solved in one nice package, rather than nuking earth and then having to hunt them down.
These time travels stories are gettin' harder to believe as time goes on, it seems like they a one trick pony, with a lot of holes. Seems like lazy writers to me, I guess.