Greenpeace had acquired the Rainbow Warrior in 1977, and by 1985 it was the most active vessel in the organization's fleet, having supported anti-whaling, anti-seal hunting, and anti-nuclear campaigns across the world's oceans. Earlier that year, the ship had relocated 300 Marshall Islanders from Rongelap Atoll, where radioactive fallout from past American nuclear tests had poisoned the land and water. From New Zealand, the Rainbow Warrior was to lead a flotilla of yachts to the French nuclear testing site at Mururoa Atoll to protest and monitor upcoming tests. France had dealt with protest vessels before, sending commandos to board ships that sailed into the exclusion zone. This time, the DGSE decided to eliminate the ship before it could leave port.

The operation involved multiple teams using false identities. Christine Cabon, a DGSE agent who had worked intelligence missions in the Middle East, posed as environmentalist 'Frederique Bonlieu' and infiltrated the Greenpeace office in Auckland, monitoring ship communications and mapping underwater approaches. Three agents aboard the yacht Ouvéa smuggled in the limpet mines. Two more agents, Dominique Prieur and Alain Mafart, traveled on Swiss passports as the newlywed couple 'Sophie and Alain Turenge,' picking up the mines and delivering them to the divers. Jean Camas and Jean-Luc Kister, the men who attached the bombs to the hull, slipped beneath the dark waters of the harbour and planted the two charges that would kill Fernando Pereira and sink the ship.

New Zealand Police launched one of the country's largest investigations. A Neighbourhood Watch group helped identify Prieur and Mafart, whose Swiss passports unravelled under scrutiny and revealed their true identities as French military officers. The other agents escaped. Cabon fled to Israel before she could be detained. The Ouvéa crew was briefly held on Norfolk Island by Australian police, but released before New Zealand detectives could make arrests. They were picked up by the French nuclear submarine Rubis after scuttling their yacht. Kister posed as a tourist, went skiing at Mount Hutt, and left the country on false documents ten days later. France initially denied everything, appointing a commission that declared the government innocent. When The Times and Le Monde published evidence that President Mitterrand had approved the operation, Defence Minister Charles Hernu resigned and DGSE chief Admiral Pierre Lacoste was fired.

On 22 September 1985, Prime Minister Laurent Fabius summoned journalists to read a 200-word statement. 'The truth is cruel,' he said. Agents of the French secret service had sunk the boat, acting on orders. Prieur and Mafart pleaded guilty to manslaughter and were sentenced to ten years in prison. Under a deal brokered by the UN Secretary-General, France agreed to pay New Zealand 13 million dollars and apologize, and the agents were transferred to the French military base on Hao Atoll for three years. Both returned to France within two years. Mafart was back in Paris by December 1987, ostensibly for medical treatment, and was later promoted to colonel. Prieur left because she was pregnant and was likewise promoted. The early releases violated the agreement, and the UN awarded New Zealand another 3.5 million dollars to establish the New Zealand/France Friendship Fund.

Fernando Pereira's death and France's betrayal of a friendly nation's sovereignty reshaped New Zealand's identity. The country distanced itself from traditional Western alliances, built new relationships with small Pacific nations, and deepened its nuclear-free stance. France conducted 54 more nuclear tests at Mururoa before stopping in 1996. The Rainbow Warrior was refloated, declared irreparable, and scuttled at Matauri Bay on 12 December 1987 to become a dive wreck and fish sanctuary. A memorial by sculptor Chris Booth stands at the bay. In 2015, Jean-Luc Kister, one of the two bombers, broke thirty years of silence. 'Secret agents don't talk,' he told a reporter, 'but he is talking.' He called the mission 'a big, big failure.' The bombing intended to silence protest. Instead, it gave the anti-nuclear movement its most powerful symbol and New Zealand a defining moment of moral clarity.