I think I finally have an idea of how I would have written it.
First, although it seems like Otaria made it out of the Phyrexian invasion mostly unscathed, the Phyrexians had in fact become aware of the continent and were planning to launch an offence against it at the end of the war. This plan never had a chance to come to fruition, but Phyrexian agents had managed to smuggle several barrels of Glistening Oil there before the war was lost and the plan abandoned. When the Mirari came to Otaria, it landed in this forgotten Oil storage. Trying to fulfill its purpose as an observing probe, the Mirari absorbed the Oil into itself, causing a terrible malfunction, which threw the entire continent into turmoil. This explains both why the probe malfunctioned and how it could have such corrupting power.
Then, when Karn turns the probe into Memnarch, it further changes the nature of the Oil, and in the process, some of it attaches to Karn. Now Memnarch is constantly trying to fight off the corrupting influence of the Oil within him, desperately holding on to Karn's vision of purity and peace. However, knowing that he himself is impure is driving him mad. He tries to stave off the madness by turning the plane into an image of order, where each thing and each being is in its own place, but still the corruption eats him from the inside. He knows that he needs Karn in order to achieve the purity he longs for, and goes to extreme lengths to find him. During this time, he can feel a planeswalker trying to enter the plane, but he can also feel that the walker is carrying the same corruption he is fighting, so he pushes him away.
Finally, when Karn manages to get through, and turns Memnarch back into the Mirari, it again causes the Oil to leak. But now it has been completely changed through Memnarch's mad power. It has been infused not only with his power to warp entire landscapes, but also by his image of how the world should look. Thus, as it starts to change Mirrodin, it does so in the image of five separate factions, just as Memnarch always envisioned the plane.
Awesome indeed.