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For the US, the Philippines are of strategic importance for control over the Pacific Ocean. From 1898 to 1946, the archipelago country was a colony of the United States. After independence was declared, the Philippines started to host US military bases and only in 1991 were they withdrawn from the state’s territory. However, already in 1998 the country signed a new agreement on the deployment of foreign troops (the Visiting Forces Agreement), and in 2014 an agreement was signed on expanded defense cooperation (the Enhanced Defense Cooperation Agreement).
The US de jure cannot build permanent naval bases in the Philippines. However, according to the above agreements, they may use Philippine facilities and stay on the islands indefinitely. In the case of crimes of any severity in the Philippines, the Americans are out of the jurisdiction of Philippine courts.
The US hopes to use the Philippines as a base for opposition against China, especially since China and the Philippines have conflicting positions on the delineation of the South China Sea
The new president of the Philippines, Rodrigo Duterte, intends to strengthen the sovereignty of his country. During the electoral campaign, he criticized the United States and in particular the extraterritorial status of the US military. After the inauguration, Duterte, speaking to Philippine Muslims, accused the US of aggression against Islamic countries and spreading terrorism. In addition, Duterte does not intend to respect “human rights” in the sense that he has vowed to physically eliminate criminals (by returning the death penalty), something which worries the United States.
What’s more, the president of the Philippines intends to negotiate with China on the South China Sea and is ready to compromise if China contributes in the island's economy. Finally, he has initiated peace talks with communist rebels whose main demand is sovereignty for the country and the withdrawal of the US military.
The US does not want to lose this state so important for dominance in the Pacific, and thus John Kerry will use any and all arguments to pressure Duterte, including economic ones. However, if the negotiations fail, the United States could impose sanctions against the Philippines or try to overthrow the new national leader by means of a coup or assassination.