Makuta is indeed on Metru-Nui. And plotting the demise of the entire island!
About this creation
The rahkshi on Metru-Nui were indeed created by Makuta. Nidhiki and Krekka were his servants, whom he sent out to find the great disks. Ahkmou did not know this, nor did any other being on Metru-Nui save one. Dume. Dume was also being threatened by the evil beings of the island. He knew that the toa would come and created a police force in advance to stop them. The vahki. The vahki were programmed not to seek out peace, but to seek out annihilation of all who opposed Makuta. So when the six destined matoran were transformed into toa, the vahki immediately knew and were dispatched to hunt them down. Five other matoran were being hunted down, and were eventually trapped and saved by the toa metru. Makuta is still confident and waits under the great temple until his tasks are complete.