On 25 August, she got underway for Manus where she supplied fuel and stores and delivered mail to ships of TF 38, the fast carrier force, 32 and 31 during the assault and occupation of the Palaus.

On 19 October, having emptied her tanks into ships scheduled to take part in the landings at Leyte, she sailed to Ulithi in the Caroline Islands, her new base.

Fleet tugs were immediately brought in to try to extinguish the fire, but in spite of their efforts, at about 09:00 the ship slowly turned over and disappeared.

Of the five kaiten sent against US ships, only one was successful, but the explosion and fire from Mississinewa was so great that the Japanese Naval Command back in Tokyo were erroneously informed that three aircraft carriers were hit.

Mississinewa was hit in the front starboard bow area, the kaiten probably released by Japanese submarine I-47 just outside Ulithi lagoon.

[1] On 6 April 2001, the hulk of the shipwreck was found by adventure divers at a depth of 132 feet (40 m) roughly 7⁄10 mile (1.1 km) north of Mogmog Island, Ulithi, Micronesia.

Officials estimated that 18,000 to 24,000 gallons of oil had been released over the course of two months, threatening coral reefs, sea turtle breeding grounds, and local fishing.

In September 2001, a dive team and contractors hired by the U.S. Navy led a survey to determine the status of the wreck and the potential for environmental damage from the deteriorating hulk.

An investigation by the South Pacific Regional Environment Programme found that the estimated 5,000,000 gallons of oil remaining in the wreck constituted an "unacceptable and ever present risk".