De-Ja II starts after two years from events of the previous game. The young researcher and archeologist Hatsushiba Ryuusuke has solved the mystery of the ancient staff and revealed machinations of the Japanese Archeological Society's director. Although he is famous now, Ryuusuke continiues his researches, and soon enough an old archeologist, Jinguuji, contacts him and asks his assistance in revealing the secrets of Palau's shrine. Ryuusuke, accompanied by Jinguuji's beautiful daughter, Himiko, is going to find the truth which is said to be able to turn the Universe from inside out...