I'm thinking that Bernard "killed" all the known hosts and transferred their consciousnesses into newly built, unknown host bodies. Of course, then they can return to them at any point if they're not destroyed (seems unlikely), or build new copies from the same designs. I think that this season will involve infiltrating human society largely undetected (with enough suspicion/being found out by a few humans to keep things interesting), with next season being the epic battle for the survival of humanity. Just a guess though.