Malacañang Service

Álvarez was later assigned to the Malacañang Palace to serve under the Governor-General of the Philippines in which he rose to the number-two position in the administrative staff as segundo official mayor.

During his service for the Governor-General, he joined the Katipunan when it was established in 1892. He then used his position to pass valuable information to the Katipunan. However, his membership was discovered when the Philippine Revolution erupted in 1896. As a result of his treason, he could have been executed or imprisoned but due to his father's influence, he was punished by sending him into a mission in Sulu to pacify a quarrel between two claimants to the throne of the Sultanate and invite them to join the Spanish Crown.

Because of his hard work of diplomacy, in 1898, the dispute was quickly agreed on a compromise and the new sultan recognized Álvarez's judgment and authority. The Sultan designated him the title Datu Tumanggung or "royal marshall of camp", the first Christian ever to attain the honor and giving him jurisdiction over the constituents of the Sultan in Basilan and Zamboanga. To mark the joyous event, a royal festival was held to which the Sultan gave Sitti Jumlia as bride to Alvarez.

There were conflicting accounts to which what happened to Alvarez after his mission in Sulu:

• According to Ronaldo Bautista, Alvarez, instead of convincing the royal houses of Sulu to pledge allegiance to Spain, invited them to organize a revolution against the Spaniards. Thus, instead of returning to Manila to report to the Spanish Government, he proceeded to Zamboanga to organize a revolutionary army.^[3]
• According to Dr. Hermenegildo Malcampo, Alvarez, after his success in Sulu, returned to Manila to report of his accomplishment in which he was pardoned by the Spanish Governor-General. He then returned home to organize his revolutionary army to topple the Spanish government in Zamboanga.^[4]

Zamboanga Revolution

In 1898, prominent Zamboangueños organized a revolutionary group to fight the Spanish that remained in Zamboanga. The council then elected Álvarez as their commanding general. He then organized an army of Christians, Muslims, and Lumads.^[5]

Alvarez, as commander in-chief, appointed his following commanders to the towns around Zamboanga:

• Mariano Arquiza – Sta. Maria
• Isidoro Midel – Tetuan
• Fruto Bucoy – Ayala
• Laureano Alfaro – Mercedes
• Melanio Calixto – aide-de-camp to General Alvarez

Under his leadership, Álvarez was able to take control of the peninsula, except the port of Zamboanga and Fort Pilar, which were fortified by remaining Spanish forces led by Governor-General Diego de los Ríos who fled from Iloilo, which was then the capital of the Spanish East Indies after Manila fell to the Americans.

After organizing enough troops, guns and ammunition, he invaded Zamboanga and engaged the Spaniards in fierce fighting. Fightings continued, consisting chiefly of artillery duels across the town and after two weeks of stalemate, General Alvarez laid siege against the Spanish stronghold of Fort Pilar in April 1899. The siege lasted a month, until May, in which the Spanish were compelled to wave the white flag. On May 18, Fort Pilar, the seat of Spanish sovereignty in southern Philippines, was surrendered to the Revolutionary Government of Zamboanga.

Republic of Zamboanga

General Álvarez then proclaimed establishment of the Republic of Zamboanga with him as its first president.

A few days before the Spanish fall, two ships boarded an American expeditionary force steamed into the Zamboanga port. Intense bombardment from the fort prevented the Americans to land. Alvarez, at the time, was attempting to recruit more troops to his army to fight the Americans.

Alvarez was even offered a sum of 75,000 Mexican dollars to turn over Zamboanga to the Americans but he turned it down. He already placed his aide-de-camp, Colonel Melanio Calixto to be acting commander of the Zamboanga revolutionary force.

However, all ended in treachery. Colonel Calixto was assassinated by the supposed orders of the commander of Tetuan, Isidio Midel. Midel, who had allied with the occupying Americans, opened the doors of Fort Pilar to the Americans. Álvarez tried regrouping his men but it was too late. On November 16, 1899, Zamboanga was officially under American hands and Midel took over the presidency, which became a protectorate under the United States.^[6]

Alvarez, betrayed, did not stopped his resolve to fight back. He then resorted to guerilla warfare and took defense of Mercedes, north of Zamboanga. The Americans, frustrated that they were unable to capture Alvarez resorted to dirty tactics in which they poisoned the water supplies of the rebels which delivered a heavy blow to the revolutionary ranks. Alvarez, in order to save lives from the Americans, fled to Basilan then to Misamis Occidental to continue the Revolution against the Americans.

He was later captured by the Americans in 1902 and sent to Manila to be imprisoned.