Here's what I believe about Makuta, the reason the Toa "defeated him," and a hint about his true form; where he got that Matoran body.
I believe Makuta is a force, a feeling, a sentient incarnation of all the dark, violent, destructive capabilities, tendencies, and thoughts of the Matoran people. He's like the Dark Side of the Force, only he's sentient and can't be used. He's there, everytime a Matoran feels anger or violence or acts upon those feelings. Makuta is there, in the heart of all Matoran, counteracted only by Mata Nui, his brother, which are the feelings of good, trust, love, etc. felt by all Matoran. The two balance each other, and neither can be destroyed. To destroy one would upset the balace of the universe; there has to always be balance.
Well anyway, I believe that Makuta has a grand scheme in mind. We don't know what it is, but we do know he has one, at least I believe he does.
I think he knew the Toa were coming for him, they had a number on his head; they wanted to off him cus all the Toa's little Matoran friends wanted to off him.
But there was no way they can do so, not without destroying everything there is in the universe, because Makuta is all the manifests of darkness in their universe, Mata Nui of light, and there must be balance.
But with these Toa constantly pestering him, Makuta can't complete his plans for Mata Nui and his people, so he has to put up a facade. He has to make it look like they destroyed him. He has to put up an act, fake his death, so the Toa would leave him alone, as well as the rest of the people of Mata Nui, so Makuta can operate his own agenda without pesky mortal pestering.
To do so, he had to assume a physical form, for the sole purpose of tossing it out there in front of the Toa to destroy it, so everyone can go on thinking that they had destroyed Makuta, where in fact they (for the sake of simplicity) just destroyed a dummy dressed like Makuta. And now that everyone thinks he's "gone," Makuta can go about his business unmolested. That is the main idea of my theory on why what happened did.
But, how to do this? How to assume this physical form, and, for the sake of screwing with the Toa's minds, a physical form they would be so caught of guard by the won't know what to do next? And to give them a convincing "going away" party?
Of course! A Matoran! That should get their little gears turning!
But how to bring this Matoran under my control, Makuta thinks.
Now, not every single Matoran is a goody-good, you all agree, right? Like there are bad humans and good humans, there are bad and good Matorans.
Makuta had to find a sutable Matoran to infest and use as a physical form, and he had to make the Matoran powerful, as well as another more intimidating physical form to use to fight the Toa as an insurance just in case the Matoran form would prove unusefull at any given time.
So he needed a Matoran, and something to create a backup physical form.
Takua later stumbles onto a hidden Golden Hau. Of course! I can use that, Makuta thinks, to create a solid forcefield/shield barrier around various piles of dead bodies and junk and conglomerate it into a physical mass. What would be more frightening than a whirling, kicking, screaming mass of body parts and junk?
So Makuta needs the Golden Hau. But how to get it. Well, like I said before, not all Matorans are good, and who would be more corrupt than a salesman?
Yes, that's right, our resident Po-Koro Koli ball vendor, who, I think, has been working for Makuta from the get-go, selling infected Kolis and what-not. Just another scheme of Makuta's for throwing a little tension and dissention into the peoples of Mata Nui.
But now that this guy has been discovered, he needs to flee, and does, but Makuta had a new assignment for him: to steal the Golden Hau.
With Makuta's wisdom, the Koli salesman finds a way to a tunnel from Makuta's lair to behind the shielded Golden Hau, and snatches it away to Makuta.
Now Makuta has the Golden Hau thanks to his treacherous little servant. But he needs this Koli salesmatoran for one more thing: a physical form.
Makuta pours all his evil essence into the Golden Hau to infect it, uses it's power to bring that kicking, screaming ball of whilring pieces to life, and also uses it to infect the Matoran, and then pour all his essence too into that poor, naive Koli ball salesmatoran too.
Then the Toa come. Makuta puts on his show, with the poor Koli salesmatoran's mind imprisoned in his own body. The first facade doesn't work, he rips the Matoran apart and kills him (with the tenticles), and then attacks the Toa with his second form, the spinning ball of oblivion, using the stolen Golden Hau's power of shielding to create a physical barrier to lift those pieces up and use them to throw at the Toa. Yes, he can do the same thing with a Matatu, but he needed a physical barrier to be able to assert his will, and that is created by the shielding power of the Hau. I very clever manipulation of its powers, I must admit.
Anyway, the Toa then fight back, knocking the Infected Hau of Makuta. Makuta looses his mask, and thus his powers to a physical form, and, to those ignorant mortals that take everthing for face value, is "destroyed." Toa leave, people rejoice, Makuta can now go about his plans, now that everyone thinks he's "dead."
Then the Bohrak come, right after Makuta's defeat.
Don't have any theories on the Bohrak and their role yet, however.
Well? Any discrepancies anyone?