You now get to choose whether you'd want Arri or Lenora to accompany you through the rest of the campaign. It doesn't really matter, as you'll be controlling the Cuotl from now on.
Now you face the Cuotl tutorial, which guides you through the basics of this fairly different race from those you already know. Follow the instructions, constructing the Reactor District and a Fane, and take over the nearby Shrine. Kakoolha, the local renegades' leader will join you. You now have to destroy the central Cuotl city (1) before the enemy takes over all of Kakoolha's cities.
Expand your territory eastwards and westwards, taking over two more cities and building more and more mines. You'll receive a message that reinforcement are coming. If you're quick and effective in economy, you won't even need them to win. Attack the enemy from the East, breaking through to the virtually defenseless central city. As simple as it gets - just storm it and you're done.
If you don't manage to do so quickly and the threat of losing is getting all to serious (meaning the evil Cuotl have taken over three cities and there's only one left), send your army to Kakoolha's capital (2) and defend it against the main enemy strike force. Now you can go straight to storming the enemy city.