I figured it out!
Mata Nui Gathers up his Glatorian, defeats Tuma, and takes command of the Skrall. They take all the giant Lego Pieces and salvage a gigantic Space Ship from it after discovering that Bara Magna is about to explode from Sun-Rays.
They then fly away from the place and arrive at a Gas Giant where the ship breaks down. Nearby in the gaseous rings around the planet Mata Nui finds a bunch of technologically-advanced Matoran-like beings who fly around on Gliders. In their society they use the great Kanohi masks as totems, and Mata Nui recognizes this. In an attempt to obtain some engineers to repair the ship, our golden hero gets dragged into the annual race championship and uncovers a secret energy smuggling ring.
Of course, Mata Nui discovers this and teams up with the locals to defeat some crazy dude who then dies, but not before setting the gas rings on fire in a chain reaction or something. So, the surviving Engineertoran hop on board with the Glatorian, and help rebuild the ship to full functionality.
Then, Mata Nui returns to his body with the navigation software, and transforms the ship into a giant robot to distract Teridax for long enough that his Glatorian, Skrall, and Engineertoran troops can invade and rescue all the captives. The group of Toa, Matoran, Dark Hunters, Skakdi, Glatorian, Skrall, and Engineertoran all follow Mata Nui's plan to shut down Makuta, then Mata Nui yanks him out and throws him into a black hole.
Finally, and with a bunch of new blood to replace all those Teridax had killed, Mata Nui sets off again on his mission.
Whatever that is.