Since there are multiple Order agents in Metru-Nui most of the final battle is held there. The Matoran and Turaga are sent away to Mata Nui above for protection, and the Makuta, Rahkshi, etc. all fight the Order agents positioned there, the Mahri, Hagah, and everyone still there (maybe even Kardas) and a few reinforcements since the ports, etc. are closed off by the Makuta.

The Makuta are trying to take Metru Nui to control it and take some control of Mata-Nui’s condition.