All six Turaga were assassinated by members of Bad Company, who were hired by the Peers. Each mercenary accomplished their mission - though with varying degrees of efficiency. The elders were replaced by their right-hand Matoran (Jaller, Hewki, etc).
Months before their assassinations, the Turaga were captured by the Makuta, who had a Parakuka attached to each of them. After their release, the elders were secured by the Island Liberation Front and brought back to their respective villages.
Much like the Makuta, the Peers wished to destroy the faith and the unity of the Matoran. so they decided that the Turaga must die. Bad Company, a group of mercenaries and assassins whom they already employed, was the obvious choice.
Matau was shot in the head by a sniper hiding in a tree during his returning celebrations.
Nuju was in the sanctum when Brykon broke in, slaughtered his guards, fought the parakuka enhanced Turaga, and finally killed him. Brykon escaped by jumping into a deep chasm and fled through Onu-Wahi.
Killed by Liacada who charged into a council meeting in the main square. She was captured after stabbing him.
The assassinations did not quite throw the villages into chaos, but did offer opportunities for other groups, such as the Toa Daedra, to rise in power. Its main effect was demoralizing the Matoran.
Before his death, Turaga Vakama hinted to Dorian and Jin that the Turaga had known who the assassins would be, and had already set plans in motion to eventually make them pay for their crimes.
Before returning to Onu-Koro, Whenua hinted at his impending death to Kehuri. Kongu learned of this later.
The Turaga were succeeded as leaders of their respective villages by influential Matoran, who became the Akiri.