Can I play as the aliens?

No. It was originally announced that in online play, you could choose to take sides either with the humans or the Covenant in netgames.

However, with the switch to the Xbox platform, the removal of online play, and other changes, this was dropped.

Players can only choose the human side in solo or cooperative play. All players are cyborgs in the other multiplayer game types, and there are no Covenant units in those games.