Ya if the flood were able to take over machines and such, then Sgt.Johnson would have been a flood awhile ago and wouldn't appear in halo 2 and 3. Plus the only reason that ship in halo 3 had flood crap is because the flood are more comfortable when they are living in there own environment and makes the reproduction process more easy, so they just terraformed the ship. I mean it makes perfect sense,. Think about the movie aliens. The reason they terraformed the outpost station is so that they can be comfortable, and make the whole reproduction process easy.