After her delivery to the Japanese Army, Yu 2 initially remained in Japanese home waters while the Army constructed additional submarines of her class and established a training program for their crews.[3] In May 1944, the Army created its first submarine combat unit (jissen butai), the Manila Underwater Transport Detachment (Manira Sensuiyuso Hakentai), consisting of Yu 2, her sister ships Yu 1 and Yu 3, and a mother ship.[3] The detachment got underway from Japan on either 28[3] or 30[2] May 1944 (according to different sources) bound for Manila on Luzon in the Philippines.[3] The vessels had a difficult voyage which included a number of mechanical breakdowns, but finally arrived at Manila on 18 July 1944.[2][3] After their arrival, the three submarines underwent repairs and thorough overhauls.[3]
On 20 October 1944, United States Army forces landed on Leyte, beginning both the Battle of Leyte and the broader Philippines campaign of 1944–1945.[3] In November 1944, all three submarines departed on their first supply run to Leyte, bound for Ormoc on Leyte's west coast.[3] Stopping at Bansaan, Yu 2 got back underway on 26 November 1944 for the last leg of her voyage to Ormoc.[3] After she transmitted a message from a position south of Ormoc on 27 November 1944, the Japanese never heard from her again.[3]
On the night of 27–28 November 1944, the United States Navy destroyers USS Saufley (DD-465), USS Waller (DD-466), USS Pringle (DD-477), and USS Renshaw (DD-499) made an anti-shipping sweep in Ormoc Bay.[3] After conducting an hour-long shore bombardment, they headed into the Camotes Sea to hunt Japanese shipping.[3] Just after midnight on 28 November, a United States Navy PBY Catalina flying boat reported sighting a Japanese submarine on the surface near Pacijan Island heading toward Ormoc Bay, and the destroyers reversed course and steered to intercept the submarine.[3] At 01:27 Waller picked up a surface contact on radar at a range of 10,200 yards (9,300 m) just off Pilar Point.[3] Waller illuminated the area with star shells and identified the contact as a surfaced submarine, and all four destroyers opened fire on it.[3] By 01:38 Waller had closed to a range of 50 meters (55 yd) and was firing at the submarine with 5-inch (127 mm) and 40-millimeter guns while the submarine attempted to return fire with her deck gun.[3] At 01:45, the submarine sank by the stern,[2][3] leaving six survivors in the water which the destroyers did not attempt to pick up because of their apparent hostile intent toward would-be rescuers.[3] The submarine the destroyers sank probably was Yu 2.[2][3]
Some historians have identified the submarine sunk on 28 November 1944 as I-46,[3] but the Japanese did not hear from I-46 after 26 October 1944 and she probably was lost in late October or early November 1944.[4] It is unlikely the U.S. destroyers encountered I-46 on 28 November, and far more likely that they sank Yu 2.[3]