My theory fits right in to the comic con promo video, right around the point where Makuta creates the mask of ultimate power (which is a horrible name). Also, let's assume that the skull spiders were an issue before Makuta and Ekimu had their fight.
Ekimu learns that Makuta has broken the sacred rule, and tries to talk his brother out of making the mask. When Makuta refuses, Ekimu secretly gathers the six village elders and shares his power of creation with them. The elders test their new creation abilities by making weapons (the ones in the sets) to fight off the skull spider hoard.
When Makuta and Ekimu fall into their self-enduced comas, the elders concentrate all their creation powers on their own raw elements, turning them into beings. For example, the protector of fire would concentrate his creation power on a river of lava, creating Tahu. (this explains why they awake with no memories)
While the Toa look for the masks of power and fight off the skull spiders, the elders begin developing their powers. While practicing with their creation powers, they receive a visit from a time traveller, who calls himself Vakama, Turaga of Fire. At first, the elders don't trust him, and engage him in a fight, but Vakama looses quickly, leaving his mask broken in half. After defeating him, Vakama explains that for many years he has been trying to finish an incomplete mask, and he finally did it.
Vakama attempts to fix his mask, but as he returns to his timeline half of his mask stays in the present. The elders study the mask, and using their powerful creation powers they fix it to an extent. They calculate that they can make two trips through time before the mask's power destroys itself again. They decide that one of them will go forward to see the outcome of the battle between Ekimu and Makuta, then return.
It is decided that the protector of fire will make the trip. When he goes, he discovers that the mask of ultimate power was so unstable, that it exploded, turning the entire planet into a ball of fire, much like a sun.
Once the protector of fire returns to his own place in time, he convinces the other elders to create an interstellar vehicle. They gather the six Toa, put them into things that would be known as Matoran Spheres and leave Okoto, just as the mask of ultimate power explodes. The elders believe that life must be preserved, and create a planet that orbits Okoto.
They give the planet elemental properties like their own, then create villagers for the planet, and call them Agori. They tell them that they are on a planet called Spherus Magna, and that they are to treat the planet with respect. Then, the elders disappear, creating more things such as the elemental lords and the prototype robot. They also eventually awake the Toa, but the spheres have diminished their bodies and erased their memories.
The elders stay in solitude for many years, creating for fun. Eventually, one elder, let's call him Velika, decides to keep watch over one of his creations.