By early 1988, Ona and his associates including his cousin Peputua Serero had formed the New PLA supported by both mineworkers and the traditional opponents of the Panguna mine Damien Dameng's Me'ekamui Pontuku Onoring. The New PLA made a number of claims including monetary compensation for the impacts of the mine, a 50 per cent share of mine revenue to the landholders and a transfer of ownership to Bougainville. The PNG Government set up an independent inquiry which dismissed the claims about the environmental impact but was critical of other parts of the mine's operation. In response, Ona established the Bougainville Revolutionary Army (BRA) which conducted numerous acts of sabotage against the mine including the destruction of the mine's power supply leading to the mine's closure in May 1989. Ona rejected an initial compromise deal by Bougainville Copper and the Government.
Ona became the acknowledged leader of the BRA after the death of Serero in 1989 with Sam Kauona, a former soldier in the army leading military operations. The Papua New Guinea Government sent in the police and then the army under Jerry Singirok to quell the uprising but they were unable to do so. The island was placed under a State of Emergency under the control of the PNG Police Commissioner while there were increased complaints about human rights abuses by PNG forces which initially strengthened support for the BRA.
In January 1990, Bougainville Copper announced that they were placing the mine in mothballs. The PNG Government announced that they would withdraw troops and for international observers to verify the disarmament of the BRA. The police fled fearing for their lives in the absence of the army while there was an attempted coup in Port Moresby over the deal.
In response to a blockade imposed by the PNG Government later in 1990, Ona declared himself to be the head of the Bougainville Interim Government declaring independence for the island. The island then descended into anarchy with several armed factions seeking power with the PNG Government supporting the militias. The BRA fell out with Joseph Kabui, the Premier of Bougainville, who had previously been a supporter.
During Prime Minister Paias Wingti's term, the PNG Government renewed military efforts with troops capturing Arawa, the provincial capital in 1993 and recapturing the Panguna mine. Sir Julius Chan, Wingti's successor tried to broker a deal but neither Ona and the BRA nor Kabui would sign a deal. Frustrated, Chan ordered a full-scale invasion in 1996 but neither Australia nor New Zealand would support it. Chan then hired Sandline International mercenaries leading to the military threatening to arrest them on their arrival and the resignation of Chan to forestall a coup.
Ona was never captured and refused to participate in the process. His forces still controlled a quarter of the island.
In May 2005, Ona disrupted provincial elections which he opposed to declare himself as "King of Bougainville" or Mekamui. He also sanctioned the establishment of a Central Bank run by Noah Musingku described by Australia's ABC TV Foreign Correspondent as a king of financial scams who established a pyramid scheme called U-Vistract. Both Joseph Kabui and Sam Kauona stated that Ona was being used by Musingku and his outsiders.
Ona died on 24 July 2005 of malaria in his village.