Shin Kaitei Gunkan (1995)

Original title: 新海底軍艦

At the end of World War II, a top-secret Japanese submarine and an American submarine have a fatal encounter and both are lost. Fifty years later the descendants of the submarines' officers are sent by the United Nations in a new secret submarine to investigate mysterious incidents in the Antarctics that could be linked to the old submarines' disappearances, and could also be the precursor to an invasion by aliens from deep inside the Earth.