The Ninjas were formed by the politician Bernard Kolélas in the early 1990s and were commanded by Frédéric Bintsamou, alias Pastor Ntoumi, when Kolelas was in exile.

After Sassou Nguesso's victory in this Civil War, Ntoumi's Ninjas fought an insurgency against his government in the Pool Department.

The conflict in the Pool escalated in a series of violent clashes in 2002-03, after which the Ninja leadership eventually gave up their armed struggle.

[2] In December 1995, the parties in the conflict signed a peace treaty where they agreed that militiamen aged 18–24 would be integrated into the national gendarmerie and police force.

[8] The Republic of the Congo Civil War began in June 1997, when the supporters of President Lissouba (including the Army and the Cocoye, Zulu, and Mamba militias) clashed with those of Denis Sassou Nguesso (including the Cobra militia and Sassou Nguesso's sympathizers in the army).

The Ninja-controlled districts of Brazzaville, Bacongo and Makélékélé therefore suffered far less casualties than the rest of the city during the first months of the war.

[8] The alliance between the Ninjas and Lissouba's Cocoyes was formalized with the founding of the Mouvement National pour la Liberation du Congo (MNLC),[7] but Ninja leaders such as Claude-Ernest Ndalla and Willy Matsanga opposed the alliance and defected with their men to Sassou Nguesso's side.

Despite the peace accords, many Ninja militiamen remained active, and engaged in robberies of civilians and train hijackings.

[11] In June 2007, Ntoumi announced that the Ninjas were "going into constructive opposition" and were determined "to work for peace in Pool and across the country".

[14] Violence continued with events such as shelling by the Congolese armed forces and attacks on trains by the Ninja militia.

Pursuant to the terms of the agreement, the Ninjas were to hand over their arms and cease their interference with trade between the cities of Brazzaville and Pointe Noire.