The Bohrok War was the period of time when the Bohrok awoke too early because of Teridax, and went on their mission to cleanse the island of Mata Nui. The Toa, Turaga and Matoran had to fight against them, in order to stop their mission for a moment, until the right time would come.
After the Toa Mata defeated Makuta, there was rumbling in the ground. Gali thought that it was Mata Nui waking up, but it was the rise of the Bohrok Swarm. The first attack by the swarm was at Ta-Koro, and a villager ran to the Kini-Nui to warn the Toa of them. He repeated one word over and over again: Bohrok. The Toa traveled to the village and encountered Kohrak and Pahrak. After defeating the threat, Turaga Vakama told the heroes that the only way to stop the Bohrok Swarms was to capture the Krana and then journey to the Bohrok Nest to defeat the Bahrag.
Fall of Le-Koro
Toa Lewa journeyed to Le-Koro to see if the Le-Matoran were alright. Le-Koro had fallen under siege by the Bohrok. The villager's masks were removed and krana were placed on them, taking control of the Le-Matoran and Turaga Matau. Lewa was then forced to wear the krana. The only Matoran who escaped the attack on Le-Koro were Kongu and Tamaru.
Attack on Po-Koro
The Tahnok headed to Po-Koro. The Po-Matoran saw the early flames of the swarm, and knew that they had to do something. Onewa proposed that Hafu, Po-Koro's greatest carver, knock down his statues that decorated the road to the village to seal of the Tahnok from Po-Koro. Hafu refused at first.
On the day of the attack, Hafu was there knocking down the statues he built to defend Po-Koro. Hewkii wanted to save Hafu from the Bohrok, but Onewa warned there was no escape. Pohatu arrived and stopped the Tahnok from destroying Po-Koro.
Other conflicts in the war
Ga-Koro was heavily damaged by attacks from the Gahlok, with the Ga-Matoran abandoning many of their homes. It would not be completely resettled until the end of the war. Ta-Koro remained mostly safe of the swarms, but Ta-Wahi suffered damage. Ko-Koro and Onu-Koro were damaged by Bohrok Swarms.
Into the Nest
The Toa then found six Exo-Toa, robotic suits the Toa could control, which they used to fight Cahdok and Gahdok, the Bahrag. During the battle, Toa Tahu realized that the Exo-Toa restricted the usage of their elemental powers, and ditched the robotic suits. Combining their elemental powers, the Toa were able to seal the Bahrag in the Nuva Cube, a special Toa seal.
After the battle, the Toa Mata fell into six pools of Energized Protodermis, which transformed them into Toa Nuva.