- —Jaller, Mata Nui Online Game
The Matoran-Rahi War, also known as the Great War, was a conflict between the Matoran of Mata Nui and the local Rahi who were, at the time, enslaved by Makuta Teridax to do his will. It took place prior to and during the Quest for the Masks, making it much more difficult for the Toa to complete the quest. Teridax was attempting to exert his control over the Matoran, and thus turned the island's Rahi against the villagers. However, guided by the wisdom and courage of the Turaga, the Matoran refused to cower to the threat. Defense forces sprung up in Ta-Koro, Le-Koro, Onu-Koro, Ko-Koro, and Ga-Koro in the forms of the Ta-Koro Guard, Gukko Force, Ussalry, Sanctum Guard, and Ga-Koro Defense Force respectively. The war lasted nearly a thousand years, throughout the Dark Time. It is unknown what name of the Po-Koro Defense, but it is known that they had one.
It ended when the Toa Mata defeated Teridax and ended the Rahi threat.
- In Le-Koro, Nui-Rama battled the Le-Matoran, carrying away villagers and taking them to their nests, where they were put to work. The Force fought back, shooting the Rahi out of the sky with Gukko Birds manned by two Matoran. Turaga Matau and many of the Matoran from the village were captured during the fighting. They remained until Toa Lewa rescued them, with help from Toa Onua.
- In Onu-Koro, the Matoran encountered tunneling Rahi who threatened the Matorans' mining work. Onepu's Ussalry rode Ussal Crabs into battle to combat the forces of Teridax. Although the city itself was at ease, the tunnels and mines were filled with danger. The Ussalry fought vailiantly against the threat, but were outnumbered greatly. At the climax of the war Onepu was unable to send even a single regiment to help Ta-Koro.
- Jaller faced massive opposition from all kinds of Rahi in Ta-Koro. Teridax poured more Rahi into Ta-Koro than any other place on Mata Nui. The Ta-Koro Guard maintained outposts all over the city and battled the Rahi everywhere they appeared. Fighting was fiercest here, with massive battles staged between the Matoran and Teridax's minions. The Charred Forest, once a peaceful jungle, was reduced to its present state due to the fighting. As Teridax infected more Rahi than ever before to attack the Matoran, Jaller saw that the Matoran could not win the war by force alone. He, along with Turaga Vakama, feared that the Rahi would overwhelm the cities soon; the Matoran could not hold much longer. The Toa Mata decided to journey to Teridax's lair to defeat the Master of Shadows and end the war, while the Chronicler's Company volunteered to make sure that Rahi did not take the Kini-Nui. Eventually, Jaller was forced to abandon most of the outer defences and fall back behind the city. Teridax ordered his Rahi to pull back from the rest of Mata Nui to destroy Takua and his friends. Jaller, Kongu, and Onepu quickly organized their forces and counterattacked the rahi at the Battle of Kini-Nui. The Matoran forces were victorious, and the Toa Mata banished Teridax temporarily, ending the war.