[2] 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.

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.

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: In 1898, prominent Zamboangueños organized a revolutionary group to fight the Spanish that remained in Zamboanga.

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

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 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.

In 1906, he was assigned to pacify Datu Ali of Cotabato and Salip Akil of Basilan in which he succeeded since his peace campaign in the Sulu archipelago before the War.

On July 3, 2008, the Zamboanga City Council approved City Ordinance 334 declaring May 18 of every year as Dia de General Vicente Alvarez and naming Plaza Roma, situated at the corner of Don Pablo Lorenzo St., Zaragoza St. and Gen. V. Alvarez St., as Plaza Vicente S.