On November 18, 1999, Iñigo Eguiluz, of Spanish nationality, a representative of the European Peace and Third World Organization, and the Colombian priest Jorge Luis Mazo, parish priest of Bellavista, Chocó, were killed in an incident involving the boat in which they were travelling on the Atrato river, in the Quibdó area, department of Chocó.

In December that year the Prosecutor General's Office ordered an individual linked to self-defense groups to be placed in preventive detention for the premeditated murder of those who died, and the attempted murder of the other occupants of the boat. The individual in question is being held in Bogotá's La Modelo prison, and is also accused of formation of self-defense groups. The gathering of evidence was ordered, to determine the possible responsibility of Carlos Castaño-Gil, leader of the United Self-defense Groups of Colombia.

On March 10, 2000, in the municipality of Sonsón, department of Antioquia, the ex Vice Minister of Youth and former Antioquia's adviser on Peace, Alex Lopera-Díaz, along with Manuel-José Jaramillo and Luis-Fernando Londoño, were detained and killed by a military roadblock as they were on their way to negotiate the release of a person kidnapped by the FARC. They were carrying a considerable sum of money.

An investigation was conducted by the ordinary justice system through a decision of the military courts, owing to the fact that the events in question had no connection with military duty. The military courts requested the Attorney General's Office to appoint a special officer to carry out the investigation.

The Prosecutor General's Office indicted an Army major, a captain, a volunteer soldier, a sergeant and a civilian driver, for the concurrent crimes of homicide and aggravated robbery, and for cover up. The servicemen involved were held at a military garrison. The Attorney General's Office preferred charges against the six members of the Army.

Following the escape from prison of one of those arrested, the Prosecutor General's Office launched an investigation and issued an indictment.