Mapenduma sits in Nduga country in Papua's Central Highlands, a region the Free Papua Movement - Organisasi Papua Merdeka, or OPM - had claimed as a theater of the long-running West Papuan independence struggle. The OPM commander Kelly Kwalik saw the WWF researchers as leverage. Within days of the seizure, he released fifteen of the Indonesian hostages. The remaining eleven - four Britons, two Dutch, and five Indonesians - he kept. The hostages were moved deeper into the jungle, to a village called Geselama. The country around them was dense montane rainforest cut by ravines, often closed by fog and rain, impenetrable to outsiders without guides.

On 25 January, the Catholic Bishop of Jayapura, Herman Ferdinandus Maria Munninghoff, made first contact with Kwalik and opened negotiations. At Kwalik's request, the International Committee of the Red Cross agreed to serve as intermediary, after consultations with the British, Dutch, and Indonesian governments. A five-member ICRC team arrived in the region on 7 February, but it took them until 25 February to reach Geselama through the weather and the terrain. They returned to the village four more times over the following weeks - late March, mid-April, early May - carrying messages, verifying that the hostages were alive, negotiating the terms of their release. The ICRC secured an agreement: on 8 May, the hostages would be set free. On that morning, Kwalik refused to hand them over.

The ICRC withdrew. Without a neutral intermediary, the Indonesian military was no longer bound by the agreement to stand down. Kopassus - Indonesia's special forces, then under the command of future president Prabowo Subianto - had already prepared for a rescue. On 9 May, Indonesian forces flew into Geselama. They entered the village in five helicopters, one of them an unmarked white civilian Bell 412 in Airfast Indonesia livery that had previously been used to shuttle ICRC staff. The OPM later accused Indonesia of having disguised the assault under Red Cross protection; the ICRC investigated and found no evidence the aircraft was marked with the emblem, but Indonesian commanders acknowledged the civilian aircraft may have confused the defenders. The village was empty. The rescue team left an observation force and withdrew. On the way out, a helicopter struck a tree and crashed, killing all five personnel aboard.

The observation team waited. On 15 May, Kopassus confirmed that the OPM had returned to Geselama with the hostages. A second assault went in. This one worked - partly. Nine hostages were freed, but two were killed by their captors as the fighting unfolded: Navy Tugiman and Matheis Yosias Lasamahu, Indonesian researchers who had come into the highlands to study the same biodiversity that Lorentz National Park would be created to protect the following year. Eight OPM fighters were killed and two captured. The rescued hostages emerged thin and exhausted, three requiring intensive care. Private military company Executive Outcomes was later reported to have provided training and operational advice to the Indonesian government for the operation.

The Mapenduma crisis never closed cleanly. Kelly Kwalik survived the rescue and continued to lead OPM operations in the highlands until he was killed by Indonesian police in Timika in December 2009. The West Papuan independence struggle continued and intensified in the decades that followed. Prabowo Subianto, who commanded Kopassus during the rescue, was elected president of Indonesia in 2024. And in 2023, almost exactly in the same country around Mapenduma, another pilot was taken captive by OPM fighters - a New Zealander named Phillip Mehrtens, whose case would drag on for nineteen months. The geography that made 1996's crisis possible made it possible again: ridges, weather, and communities whose consent determines who moves through these valleys.