1.yes, he's now fighting for human species cuz the remnants of umbrella is
controlled by the red queen, in essence, it's more of a matrix kind of
machine versus human kinda of battle.
2.Jill is controlled by that spider shaped thing on her breasts, everybody
else is just a clone purposely injected with selective memory, depending on
their role.
3. Red Queen
4. Sorta, red queen is just the computer system, she got crazy after the
original incident at Raccoon city, her take-over of umbrella is the slow
process, at least in the first few installations, umbrella was not under her
control.
5. He and Alice are humans merged with virus on a cellular level, both she
and he are only partially human, but human nonetheless, red queen, on the
other hand, is pure computer program with the sole purpose of eliminating
the whole human race as an species, hence he fights against her, at least
that's the explanation given by the plot.
6. Humans are on the verge of extinction, and Alice is the only human
successfully merged with T-virus, he's giving her power back to her, to save
human species.