Alvarez had been organizing since March 1898, taking control of most of the Zamboanga Peninsula while the Spanish held the port and the fortress. His coalition was remarkable for its diversity. Felipe Ramos served as Captain, Melanio Calixto was promoted to Major, and Captain Gowito Sebastian commanded companies alongside them. Together they formed the Revolutionary Council and the Zamboangueno Revolutionary Government. This was not merely a military operation -- it was an assertion of self-governance by people whom the Spanish had divided along religious and ethnic lines for over two centuries. That Christians, Muslims, and indigenous Lumad fought side by side against the colonizer remains one of the most striking facts of the Philippine Revolution.

The first blow fell at Santa Barbara, where revolutionary fighters used native fishing boats to slip past the Spanish defense line and land below the barrio's wharf. They evacuated residents and set the neighborhood ablaze to deny cover to the defenders. Alvarez then pulled back, leaving sentries to keep watch over the Spaniards inside the fort. The full assault resumed on April 27, 1898. Realizing they were exposed, the Spanish troops withdrew behind Fort Pilar's walls for a final stand. For three days, gunfire echoed across the waterfront. When Spanish artillery began to falter, the revolutionary forces intensified their bombardment.

Alvarez offered terms through Captain Sebastian: surrender, free passage to Manila, and an end to hostilities. General de los Rios refused, citing international protocol, but asked that civilians and dependents inside the fort be allowed to leave. Alvarez agreed on the condition that no military personnel escaped with them. The evacuation took several days. Those with wounds were carried out on litters; Zamboangueno families who chose to stay were relocated to the suburbs. Once the civilians were clear, the truce dissolved. By May 10, Captain Ramos had positioned forces along the delta while Major Calixto's men sealed the beach approach near the aqueduct. The fort was surrounded on all sides.

On May 17, 1898, a white flag appeared above the breastwork. General de los Rios, badly wounded in the knee and supported by an aide, stood in formation as his troops lined up in the square with their rifles piled before them. The following morning, Alvarez entered the fort with Calixto, Ramos, Sebastian, and Isidro Midel. De los Rios saluted Alvarez, who returned the courtesy. Then de los Rios handed over his saber -- the symbol of Spanish sovereignty -- in an elaborate ceremony that ended more than two and a half centuries of colonial rule in Zamboanga.

That same day, General Baldomero Aguinaldo, cousin of President Emilio Aguinaldo, arrived carrying a presidential message confirming Alvarez's title as General of the Philippine Revolutionary Forces. The Republic of Zamboanga was born. On May 23, the Spanish departed for Manila aboard the S.S. Leon XIII. General de los Rios succumbed to his wounds during the voyage, the last Spanish governor of Mindanao dying at sea. The republic he left behind would itself prove short-lived -- American forces captured the fort six months later -- but the siege had demonstrated that Mindanao's peoples could unite across the lines their colonizers had drawn.