In November the gunboat helped escort an Army Expeditionary Brigade under Brigadier General Lloyd Wheaton to San Fabian in Lingayen Gulf, then firing on insurgent entrenchments on the landing beaches.

Admiral John A. Schofield, then an Ensign commanding Samar, later wrote the gunboat captured a banca in a cove off Paragua and rescued two "fair young maidens" who had been kidnapped by bandits from the town of Puerto Princesa.

Recommissioned on 19 June 1902, Lt. Montgomery M. Taylor in command, Samar steamed south to Zamboanga, Mindanao, where she carried messages and stores for Marine detachments assisting the Army in suppressing the Moro rebellions among the southern islands.

Recommissioned on 11 March 1908, Ensign Reed M. Fawell in command, Samar was assigned to the Pacific Fleet's Third Squadron, which mainly patrolled the Yangtze River and along the Chinese coast in the vicinity of Guangzhou.

Every year the gunboat also sailed north to Nimrod Sound, outside Ningbo, Zhejiang province, for target practice near the Imperial Chinese Navy's gunnery school.

Returning upriver, the gunboat reached Hankou in August and Yichang in September where she wintered over owing to both the dry season and the outbreak of rebellion at Wuchang in October 1911.

Following the collapse of the Qing dynasty and the declaration of the Republic of China by Sun Yat-sen that winter, tensions eased and the gunboat turned downriver in July 1912, arriving at Shanghai in October.