The Justiciars were originally the judicial system of Yheyn, though that now falls under the juristiction of other, less powerful beingss. Their leadership, the actual judges, was composed solely of Turaga, though most members who fought for the organization were Matoran.
Around 3100 PL, the Count of Yheyn, Gauraur, acted against the Justiciars, who had gained almost complete power over the island, and had begun abusing it. He was executed by their soldiers, and they held a reign for some 200 years after that.
Eventually, the island was taken back from the Justiciars some 200 years later by a young Toa named Gremost. The Onu-Toa managed to gather a group of Matoran and other Turaga to his side and led a massive coup against the Justiciar forces, killing most of their leaders in a single night.
However, that did not mean that they had been defeated permanently. It took decades, but eventually the Justiciars were pushed back until they old held one bastion of power - their base, Overlook Courthouse, on the island of Nibar. Even after that, remaining loyalists made assassination attempts and attempted to gather their own rebellions after Gremost was appointed to Count. It would not last, however.
Present day, the Justiciars are gone. Many of the natives still remember them, but none with fondness. They are a relic of the past most would prefer never returned.