"Apart from hypoxia, are there any other scenarios that would account for the crew and passengers being incapacitated AND the plane being able to fly for another 5-7 hours?"
rabidstoat: "Surely there are. Off the top of my head, hijacker(s) with threat or use of force."
What I meant was: are there any other scenarios apart from hypoxia that don't involve foul play of some type. I'm struggling to think of any.