Okay so, in summary:
>While the Karzahni was intended to be sentient and as such made no effort to hide it, in this AU the Morbuzakh was accidentally made sentient but hid this from Teridax. The Karzahni was discarded and wound up deep underground, more or less like normal.
>The Morbuzakh did its work screwing up Metru Nui real good, but secretly contacted the Karzahni, and together created a means of infesting and controlling MU inhabitants, known as Seeds. The OoMN also planted several agents in Metru Nui to watch over the Morbuzakh in case the infestation got too far out of hand.
>Lhikan was not captured by the Dark Hunters, escaping as Vakama managed to wrest himself free and slow his descent with, of all things, a Morbuzakh vine.
>An OoMN agent discovered the masses of stored Seeds the Morbuzakh had created, and despite its best efforts to kill him he escaped. Not wanting its plan to be discovered, the Morbuzakh acted, releasing thousands of spores around the same time the Toa Metru were created. Hundreds became thralls of the Morbuzakh, including swathes of the Vahki Force. Ta-Metru had survivors in the single digits; Po-Metru suffered the least. Teridax, as Dume, locked down the Coliseum.
>The Toa Metru raced to find the Great Disks with Lhikan's help. The Dark Hunters attempted to ambush them, but in the ensuing conflict Krekka fell into a pit of molten Protodermis. Nidhiki attempted to flee, but was enthralled by the Morbuzakh. Around this time, Ko-Metru is fortified with bunkers and trench lines to fend off the waves of infected Matoran, Rahi and Vahki. Ga-Metru closed off all entrances to Ta-Metru and it too became a fortress district. Le-Metru was lost in days. The lower levels of Onu-Metru were lost, but the higher levels were successfully defended. Po-Metru became one giant refugee camp.
>The Toa Metru assaulted the Great Furnace in an effort to kill the King Root, and Teridax, knowing the danger, sent a surviving Vahki force to assist them, though this was steadily thinned to nothing as they fought their way through Ta-Metru. However, in the battle with the King Root Nidhiki attacked, and though outmatched he managed to allow more infected in. Onewa accidentally killed the infected Dark Hunter, and although they fought hard, only Nokama and Whenua escaped the Great Furnace alive, though Nokama was seemingly killed by the now-enthralled OoMN agent who had discovered the Morbuzakh's plan. Whenua escaped Ta-Metru alone, distraught and defeated.
>Onu-Metru invents the flamethrower. While the Morbuzakh itself feeds on fire, its Seeds are too small and vulnerable to enjoy the same resistance, and these weapons are capable of driving weaker infested back, lightening the load on Onu-Metru defenders and allowing them to assist the war effort in Ko-Metru. However, the flamethrower proved inefficient in Ko-Metru, and the Onu-Matoran got to work on a 'frostthrower'. Nokama reappeared at the so-called 'Fire Gate', the last surfaceside route to Ta-Metru. Lhikan was suspicious, but allowed her to be taken to medical attention. The frostthrower prototypes are mixed; they had less of an effect on the Seeds but could weaken the Morbuzakh vines considerably. These help the Ko-Matoran drive the infected back, and scientists begin working on a way to safely free an individual from Morbuzakh control.
>The Morbuzakh betrays Karzahni, and despite the Karzahni's superior intelligence it is no match for the much larger and more powerful Morbuzakh. However, a small piece of it survives. Nokama proves, as Lhikan suspected, to be infected when she suddenly destroys several guard positions and emplacements, as well as the Fire Gate before she is subdued by Lhikan. To keep back waves of infected from Ta-Metru, defenders are forced to destroy the bridge. The Morbuzakh decides the effort is no longer worth it, and withdraws from Ko-Metru, allowing the Ko-Matoran to celebrate a somewhat hollow victory. Scientists discover a cure for Morbuzakh infection, and Nokama is the first to be freed, though she remains in critical condition. Deep underground, the Karzahni found the discarded corpses of the rest of the Toa Metru, inhabiting and seemingly 'reanimating' Toa Nuju.
>Lhikan, Whenua and a couple of heavily armed Matoran volunteers headed into Ta-Metru's underground through Onu-Metru in an effort to find a Mask of Healing and the Great Disks. They are attacked by the infected OoMN agent and several infected Vahki. The fighting is brutal, but they are saved by a storm of discarded masks and other objects cutting down their attackers. Their saviour appears to be a rather dismissive Nuju, who plucks a Mask of Healing from the OoMN agent, whom was using it to heal his own injuries somehow. 'Nuju' sends the Matoran back with the mask while the Toa press on, 'Nuju' recovering the Great Disks as the Morbuzakh attempted to dispose of them with his Matatu, and the Toa flee, Whenua bringing the tunnel down behind them to block pursuing infected.
>Lhikan alerts the Onu-Metru forces, and 'Nuju' is surrounded, where the Karzahni explains its need for his body, and wants the Morbuzakh dead just as much as they do. Meanwhile, the Morbuzakh attacks Po-Metru. Before the attack can be driven back, untold numbers of Matoran are dragged off screaming, where they are presumably infected in order to bolster the Morbuzakh's forces. Nokama is healed, but still incapacitated. Teridax alerts Karzahni of all the remaining routes to the Great Furnace, and the Morbuzakh in retaliation hits the Coliseum with most of its forces. Teridax, knowing the Coliseum will not hold them, abandons his body and finds the infected OoMN agent underground, and drives the Seeds from his body, only to possess them himself. Another agent arrives to investigate the loss of communications with their contacts in Metru Nui, but they are infected, and leave the island with enough Seeds and vines to start an infestation elsewhere. Nokama recovers, and agrees to help defeat the King Root.
>The Toa press through the underground, and Teridax, knowing their efforts may be the last one Metru Nui can make, opens and closes various doorways remotely to minimise resistance before he is driven off by the Morbuzakh and its forces. The Toa reach the King Root, only this time most of its forces are unavailable, still at the Coliseum, and using the Frostthrowers manage to freeze the King Root solid, Whenua and Karzahni combining their powers to bring the Great Furnace down on it, slaying the King Root. The Morbuzakh itself is killed(though the roots sent off island survive) and the infected lose any form of coordination, making them much easier to contain, round up and cure. Teridax and Karzahni both quietly leave Metru Nui, as the Matoran begin slowly rebuilding.
Okay yeah thats a loose use of the term summary but there you go. Nothing written beyond that.
An RP in the setting might be cool, actually.