The flood will be in the game, it makes sense, the covenant fought the flood in numerous occasions(read the books) and listen to all the cinematics in the Halo series, however the humans made it plain who the flood were in CE because of the data collected by Cortana and John 117, and if you watch the Halo Wars cinematics and watch the cut scene which first features the Arbitar(not the arbitar you all come to hate and love in Halo 2 and Halo 3) an Elite asks him about the infection(tada) which is also known as the flood, and to answer the question if the flood can steal vehicles, they can, but in order to do so, they must kill a host who knows how to operate the vehicle it stole(Yes the flood not only infects your body it takes and uses your knowlegde and memories, so yes they did know the location of Earth before the covenant, they just didn't have the ability to get there)so yes the flood might steal your vehicles in Halo Wars, so better polish up on those infantry tactics and capabilities, you are going to need them
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