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In July 1898, three months into the Spanish-American War, U.S. command began suspecting Aguinaldo was secretly negotiating with Spanish authorities to gain control of Manila without U.S. assistance, reporting that the rebel leader was restricting delivery of supplies to U.S. forces. General Thomas M. Anderson assessed that a rebel controlled Manila would be able to resist any U.S. attempt to establish a provisional government. General Wesley Merritt disregarded an Aguinaldo warning not to disembark American troops in places liberated by Filipinos without first informing him in writing about the places and purposes of the actions. U.S. commanders came to suspect that Philippine rebel forces were informing Spanish forces of U.S. troop movements.

U.S. and Spanish commanders negotiated a secret agreement to stage a mock battle in Manila, after which Spanish forces would surrender to U.S. forces. Philippine rebels would not be allowed to enter the city. Fighting between U.S. and Philippine troops almost broke out as the former moved to dislodge the latter from strategic positions around Manila. On the eve of the staged battle, Anderson telegraphed Aguinaldo, "Do not let your troops enter Manila without the permission of the American commander. On this side of the Pasig River you will be under fire." On August 13, U.S. forces captured Manila. Relations between the U.S. and Philippine rebels continued to deteriorate.

Trimmings
"The officers of the United States Army who believed that the insurgents were informing the Spaniards of the American movements were right. Sastrón has printed a letter from Pío del Pilar, dated July 30, to the Spanish officer commanding at Santa Ana, in which Pilar said that Aguinaldo had told him that the Americans would attack the Spanish lines on August 2 and advised that the Spaniards should not give way, but hold their positions. Pilar added, however, that if the Spaniards should fall back on the walled city and surrender Santa Ana to himself, he would hold it with his own men. Aguinaldo's information was correct, and on August 2 eight American soldiers were killed or wounded by the Spanish fire."
 * On July 9, General Anderson informed Major General Henry Clark Corbin, the Adjutant General of the U.S. Army, that Aguinaldo "has declared himself Dictator and President, and is trying to take Manila without our assistance", opining that that would not be probable but, if done, would allow him to resist any U.S. attempt to establish a provisional government. On July 15, Aguinaldo issued three organic decrees assuming civil authority.
 * On July 18, Anderson wrote that he suspected Aguinaldo to be secretly negotiating with the Spanish authorities.
 * In a July 21 letter to the Adjutant General, Anderson wrote that Aguinaldo had "put in operation an elaborate system of military government, under his assumed authority as Dictator, and has prohibited any supplies being given us, except by his order", and that Anderson had demanded that Aguinaldo must aid in fulfilling Anderson's demands for necessary supplies.
 * On July 24, Aguinaldo wrote a letter to Anderson in effect warning him not to disembark American troops in places liberated by Filipinos from Spain without first informing him in writing about the places and purpose of the action. Murat Halstead, official historian of the Philippine Expedition, wrote that General Merritt remarked shortly after his arrival on June 25: "As General Aguinaldo did not visit me on my arrival, nor offer his services as a subordinate military leader, and as my instructions from the President fully contemplated the occupation of the islands by the American land forces, and stated that 'the powers of the military occupant are absolute and supreme and immediately operate upon the political condition of the inhabitants,' I did not consider it wise to hold any direct communication with the insurgent leader until I should be in possession of the city of Manila, especially as I would not until then be in a position to issue a proclamation and enforce my authority, in the event that his pretensions should clash with my designs."
 * U.S. commanders suspected that Aguinaldo and his forces were informing the Spaniards of American movements. U.S. Army Major John R. M. Taylor later wrote, after translating and analyzing insurgent documents:
 * The secret agreement made by Commodore Dewey and Brigadier General Wesley Merritt with Spanish Governor-General Fermín Jáudenes and with his predecessor Basilio Augustín was for Spanish forces to surrender only to the Americans. To save face, the Spanish surrender would take place after a mock battle in Manila that the Spaniards would lose; the revolutionaries would not be allowed to enter the city.
 * Before the attack on Manila, U.S. and Filipino forces had been allies in all but name. After the capture of Manila, the U.S. and Spain formed a partnership that excluded the Philippine rebels. Relations continued to deteriorate, however, as it became clear to Filipinos that the Americans were in the islands to stay.