Also, to go further on the Skall, the second type (the type that doesn't discriminate and only tolerates other of it's kind) can also be an early product of one that is produced in the lab.
OK, here comes my short story:
During this war with the Krall (or maybe something else if that's decided), the Skaarj are working on a new type of Skall (or whatever) and this new type is the first of it's kind. An idea of what kind: the kind that is not easily killed and this is not because of it's huge health or size. Regen-batteries and energy-absorbtion from energy-bases projectiles (like shockprojs). Recharging makes them harder to kill, and makes it for them easy to kill you.
Think of directly linked energybased weapons on their limbs or linked staffs (Krall) which become more powerful when more energy is available to disperse. This new type of creature (which can also be a suped-up Skall, see my post above) is then scheduled for production to be used in the war. Only, for the sake of the mod, the Skaarj made some crucial mistakes: underestimating their own technoligy again making silent communication possible between their newly created kind. This new species so to speak doesn't have any memories of what they were before (like Krall, Skaarj, Brute, Nali, Pupae, Slith or whatever) and can't believe that the Skaarj are their masters. They silently team up and during your own escape, the base is suddenly attacked from within. The next-gen labrats slowly take over the entire facility and doing so, you primary enemy will slightly change from Skaarj to this new species, with in the end maybe some ultra-prototypes which were set free by attacking force.
One more note about this new species: they only 'trust' each other and hate everything else. So you have Nali, Brute, Skaarj and Krall-like creatures fighting alongside each other as they were the same species, because of the forced memoryloss the Skaarj induced.