Proceeding to the Flores Sea, "Thresher" intercepted a three-ship convoy escorted by two anti-submarine vessels on 21 February. One of the sub's two torpedoes hit the stern of a transport. "Thresher" then evaded 13 depth charges before returning to periscope depth a little more than an hour later. She observed her target lying dead in the water while barges lightered troops to an undamaged mate. As escorts searched the waters nearby, "Thresher" closed and torpedoed the second transport, which had stopped to transfer survivors. Two loud explosions reverberated in the background as the boat dived to avoid possible countermeasures.