I think one of two ways:
1) Kellhus makes it into the Ark and finds renderings of the Nail of Heaven, which is indeed a mother ship the Inch can't control with the damaged Ark. He then teleports himself to the mother ship, finds a storage locker full of charged plasma cannons, and teleports back. Problem solved.
2) Much more likely, because I believe Kellhus will be the final soul needed to resurrect the No-God and he will therefore be unavailable to save the world, Mimara will invert the chorae on the carapace, causing the No-God to implode. The implosion will also have the added benefit of keeping a new Indigo Plague from spreading across the Ordeal. This will probably happen in the last series because I think the UC will end with Kellhus's death and the No-God's return.