Freeport became interested in West Papua in the 1950s, and in 1965, negotiations between Freeport and Indonesia began one month after a military coup and widespread massacres brought General Suharto to power. Freeport was the first foreign corporation to sign a deal with Suharto's regime. The 1967 agreement gave the company broad powers over the local population and resources, including the right to take, on a tax-free basis, land, timber, water, and other natural resources, and to resettle indigenous inhabitants while providing reasonable compensation only for dwellings find permanent improvements. Under the new Indonesian regime, the indigenous population had no rights of refusal or of informed consent, nor any right to adequate compensation. A sign of the times, no social or environmental impact assessment was done.
The two main communities impacted, the Amungme and Kamoro, numbered several thousand people, organized in clan-based village social and governance structures. With lands encompassing the areas tropical rainforest, coastal lowlands, and glacial mountains and river valleys, the Kamoro (lowlanders) and Amungme (highlanders) practiced a subsistence economy based on sustainable agriculture and forest products, fishing, and hunting; their cultures intimately entwined with the surrounding landscape.  Resistance to Freeport and other colonizers began immediately. This has taken the form of armed attacks against the mine and its workers. In 1977, the OPM blew up an important pipeline, shutting the mine down for several days.
The ecology of West Papua is one of the most biodiverse places on Earth, with up to 7% of all plant and animal species being found there. Freeport's mining operation in West Papua has destroyed this environment, which the Amungme and Kamoro hold sacred and subsist on. The mine has taken 120 meters off of the top of a sacred Amungme mountain. Freeport dumps millions of tons of silt-like tailings into the local river system, polluting it with metals and turning a miles-wide lowland river area into a dead, barren landscape. The river is now almost entirely devoid of any life. They pile toxic waste rock thousands of feet high at dumpsites in the surrounding area including at a sacred lake used by the Amungme. Filling valleys with mine waste that leaches copper, acid, and mercury into the ground, they have polluted springheads tribal people miles away use for drinking water. The rainwater run off from these toxic landfills has resulted in even more pollution. Local people have died when Freeport poisoned the water people drink, and the piles of waste have resulted in landslides. While landscape reclamation projects have begun at the mine, environmental groups and local inhabitants are concerned with the potential for copper contamination and acid mine drainage from the mine tailings into surrounding river systems, land surfaces, and groundwater.
In 1977 the rebel group Free Papua Movement attacked the mine. The group dynamited the main slurry pipe, which caused tens of millions of dollars in damage, and attacked the mine facilities. The Indonesian military reacted harshly, allegedly killing at least 800 people.
By the mid-1980s, the original mine had been largely depleted. Freeport explored for other deposits in the area. In 1988, Freeport identified reserves valued at $40 billion at Grasberg (Dutch, Grass Mountain), just 3 kilometres (1.9 miles) from the Ertsberg mine. The Grasberg Mine is the largest gold mine and the third largest copper mine in the world.
In 1996, Tom Beanal, a leader of the Amungme people of West Papua, filed suit against Freeport-McMoRan in US federal court. Beanal alleged that Freeport was complicit in human rights abuses committed against him and the Amungme people by security forces employed by Freeport; the human rights violations alleged were surveillance, mental torture, death threats and house arrest. Beanal also alleged that Freeport's operations in West Papua caused severe degradation to the Amungme's environment and habitat. Finally, Beanal alleged that Freeport's mining operations resulted in 'cultural genocide' by destroying the Amungme's habitat and religious symbols.
The same year, Yosefa Alomang also filed suit against Freeport-McMoRan in Louisiana state court. A mother of six, Alomang became a leader in the fight against Freeport in reaction to military action against the local population when hundreds of Amungme people cut a Freeport pipeline. The protest had itself resulted from the killing of thirty people after a peaceful protest. Bombs and bullets then totally wiped out Waa and Kwakmi villages - and villagers fled to hide in the forests. She protested, filed lawsuits, worked to free imprisoned activists, and more for years . Alomang also set up a women's cooperative called Kulalok that destroyed produce that Freeport important so that Freeport would be forced to pay attention to them and buy local goods. She also founded Yahamak, the Foundation Against Violence and for Human Rights. The work she did with them earned her the Goldman Prize as well as a $248,000 reward from Freeport in 2001 for a clinic, meeting hall, orphanage, and human rights violations monument. However, Alomang continued protesting against Freeport because a major pit collapse at the Freeport's giant Grasberg mine killed 9 workers in 2003 .
WALHI (Friends of the Earth Indonesia) won a landmark case against Freeport in 2001. The case, filed in the South Jakarta District Court, found the company guilty of violating Indonesian environmental law for their role in the May 2000 landslide at the Wanagon Dam. WALHI accused Freeport of deliberately concealing information about the landslide and giving false and inaccurate explanations to the public. Freeport’s press releases blamed the slide solely on heavy rainfall, but Indonesia’s environmental protection agency, Bapedal, found that Freeport had been dumping twice the permitted amount of waste at the dam prior to the slide. The court ordered Freeport to minimize the risk of more rock slides at Wanagon and to reduce the creation of toxic waste to comply with water quality standards .
In February and March 2006, residents shut the mine down for several days while students demonstrated in the provincial capital of Jayapura and in Jakarta. Police injured and killed several of the protesters .
But justice was not served on the Amungme. By 2014, Freeport's target was to sell 2,118,525 tonnes of copper concentrate from its Grasberg mine in Indonesia this year. The concern was to build a smelter, to refine copper because of Indonesia's ban on concentrate exports, and also a higher export tax. In 2021, Arizona-based Freeport-McMoran has nearly doubled copper and gold production at its landmark Grasberg mine following a ramp-up from depressed COVID operations .
Papuans continue to face violence and intimidation from. Inhabitants of the villages that surround the mine are prevented from taking trips to the forest to hunt or to their vegetable gardens, which are frequently far from their homes. The military accuses anyone leaving of being terrorists. Many of the residents face starvation and malnutrition without their staple gardens and hunted meat. This situation is part of a larger system of oppression by the Indonesian government of the West Papuan people since the “Act of Free Choice.” Citizens who express cultural identity such as singing songs in the local language or advocating for the preservation of traditional lands are labeled “separatists” and are subject to imprisonment, torture and even murder .
Since then, the conflict has also increased gender-based violence, most commonly though not exclusively targeting women and girls. Environmental factors have disproportionate factors on the indigenous women battling against the extractive industry in a conflict-prone territory. Women and children as young as three years old have been raped by soldiers. This feeds into a wider sense of fear and insecurity among the indigenous communities because thus use gender-based and sexual attacks against Papuan women in general, and defenders of human and environmental rights in particular to terrorize and stigmatize locals and their families [2, 4].