Bai Ali Indayla, a human-rights worker and antimilitary activist, has met just one American soldier. They convened at a picnic table inside a Philippine army camp in Mindanao in 2010 to discuss the alleged suicide of a Filipino who died under mysterious circumstances after starting a job with the U.S. military’s counterterrorism program. Indayla believed the death was suspicious, and she wanted answers, but her first and only interaction with a U.S. soldier earned her none. He was dismissive, she says, as well as arrogant and profane. After a brief and terse exchange, he walked out of the meeting without warning, and she walked away with all of her prejudices soundly affirmed.

The encounter, colored by her mistrust and his apparent indifference, reflects an enduring dynamic at play between two forces in Philippine society: the U.S. military, whose decades-long occupation of the islands eventually gave way to civil unrest, and a small but historically significant network of activists who believe the former’s presence is tantamount to neocolonialism. As China more aggressively asserts its claim over the South China Sea and the U.S. ponders a “pivot” to Asia, the gap between these groups seems to widen, calling fresh attention to the question of U.S.-Philippine ties. (PHOTOS: The U.S. Military in the Pacific)

The relationship between ordinary Filipinos and U.S. armed forces is a tortured one, dating back to America’s “liberation” of the Philippines from colonial Spain more than a century ago. The U.S. takeover of the Philippines in 1899 kicked off a short, bloody war, during which Filipinos were forced into reconcentrados (a type of concentration camp), massacred in their villages and subjected to a new torture technique now known as waterboarding. When the U.S. finally gave the Philippines its independence in 1945, sprawling American military bases remained — and with them, an exploding sex industry and a legacy of human-rights violations widely publicized by the national press.

A decades-long antimilitary movement culminated in the 1991 closure of American bases and the ousting of U.S. troops. Yet American forces have nevertheless maintained a limited but continuous presence in the country, where they conduct regular joint training exercises and have, in recent years, extended antiterrorism efforts. Dubbed “the second front of the war on terror” in 2002, western Mindanao has played host to 600-strong U.S. troop rotations as they pursue two al-Qaeda-linked terrorist groups. Though officially base-less, barracks, ports and communications infrastructure emerged within and near the Philippine military camps that host American soldiers. This year, the Aquino administration granted the U.S. Navy permission to use the former U.S. base in Subic Bay for the service of U.S. warships.

The situation is now being complicated by China’s claims to the South China Sea, a large shipping channel that boasts enormous, untapped oil and gas reserves. Some Filipinos, including President Benigno Aquino III, see the disputed territory as essential to both the territorial and economic security of the country. For them, the U.S. stands to be a strategic partner that is uniquely positioned to help them counter Chinese power. The Philippines accepted $11.9 million in military aid last year and another $30 million in 2012. In light of the territorial dispute with China, the U.S. has further committed to help the Philippines build “a minimum credible defense posture” and a coastal monitoring system.

(MORE: U.S. Takes a Pass — for Now — on China Sea Disputes)

To a growing chorus of contemporary critics, however, the prospect of an American “pivot” reads as a warning against an expansive military presence just 20 years since the closure of American bases. For them, the relationship between the U.S. armed forces and Filipinos is defined not by defense, but by a legacy of human-rights violations and the perception that U.S. soldiers are above Philippine law. The China threat, they argue, is a bogeyman used to justify an ongoing U.S. presence and draw the public’s attention away from its societal cost. Most of those affected by the most recent operations have been Muslims in Mindanao, a historically disenfranchised group that is, in many ways, isolated from Manila and somewhat invisible to the public. The death of Filipino interpreter Gregan Cardeño in 2010 put a national face on the issue of militarization in Mindanao. Cardeño was found hanged in a U.S. Army barrack in Mindanao, two days after beginning a new job with American soldiers. Authorities ruled his death a suicide, but Cardeño’s family continues to cry foul play. “Incidents like the Cardeño case have built up a kind of consciousness and attitude about even a very limited U.S. presence,” says Roland Simbulan, a professor at the University of the Philippines. (MORE: China’s Territorial Ambitions Give Renewed Impetus to a U.S. Presence on Okinawa) Indeed, there seems to be growing dissatisfaction with where things are headed. On April 16, U.S. and Philippine troops launched the largest iteration of the Balikatan War Games in the event’s history. More than 4,500 U.S. soldiers participated in the military exercises, with observers from Australia, Indonesia, Malaysia, Japan and South Korea present. In response, 50 students in Manila defaced the American seal at the U.S. embassy and burned an American flag. Activist groups and political-party leaders led hundreds of demonstrators on a caravan to Clark Air Base, a former U.S. military outpost. In Mindanao, Indayla and her colleagues organized thousands of protesters in demonstrations that spanned seven cities and 10 days. The death of a fisherman killed after a U.S. Navy vessel collided with his boat on April 18 deepened the tension, sparking sympathy protests in Los Angeles, San Francisco, Seattle, New York and Hong Kong.

While continued projection of U.S. military force in Southeast Asia seems certain, the hearts and minds of Filipinos are not. Even the Philippine Senate is divided on the issue, with a vocal faction advocating the revocation, or at least the reconsideration, of the Visiting Forces Agreement (VFA). “It’s not a black-and-white battle,” says Philippine Senator Miriam Defensor Santiago. While she has long called for an end to the VFA and the establishment of an “independent foreign policy,” she recognizes that U.S. militarization in the Philippines is an inevitability, given the geopolitical climate. “What is the alternative if we want to kick out the Americans?” she says. “Are we going to fall under the thumb of China?” A better solution would be to amend the VFA to safeguard against military abuses and limit the autonomy of troops on Philippine soil, she says.