"Seal" arrived at Soerabaja on 5 February. Daily air raids necessitated diving during the day and precluded repairs to her engines, which smoked excessively, and to the broken prism control mechanism in her high periscope. On 11 February, she departed for Tjilatjap on the south coast of Java, and on 14 February, she went alongside . That same day, the Japanese moved into southern Sumatra, and on 19 February, they invaded Bali. Allied forces counterattacked, and as air and surface forces hit the Japanese fleet, "Seal" departed Tjilatjap and transited Lombok Strait to patrol north of Java. On 24 February, she attacked two convoys, only damaging one freighter. The next day, she unsuccessfully attacked an enemy warship formation. On 1 March, as the Japanese moved against Soerabaja, she was similarly disappointed. On 14 March, she headed east to patrol the southern approaches to Makassar City, and for the next week, with her forward air conditioning unit broken down and her refrigerating plant inoperable, she patrolled between that city and De Bril Bank. On 21 March, she headed for Fremantle, Western Australia—the Netherlands East Indies had fallen.