I'm really hoping that the Helghast start using some sort of strange organism (biological warfare). Like they start capturing ISA Soldiers and the organism turns them into flood-type parasite/monster things? I mean, it's stolen from Halo, but who says Halo didn't steal the idea from some other game?
Hypothetical Situation: You get captured and sent to a Helghast prison, and once you wake up the place is overrun by monsters/zombies! And you fight through the level for 30-45 mins until you find your squad (which was trying to find you).

It would make Killzone 2 my favorite FPS then (current is Timesplitters: Future Perfect).