The Japanese are one of the 41 civilizations in the default game. It's also possible to port all of the Samurai Mod from the original game into the Japan-Korea map to play out that scenario on its real world map but no one has ever uploaded that scenario.
Japan was unified in the 1600s from then and for about 200 years until the late 1800s the country was in a period of isolation and technology rarely changed until the country became modernized. From the late 1800s to the year 1945 the country went though a massive expansion and then contraction after the world wars were fought. After the year 1946 eventually some of the nearby islands were returned to Japan such as the Bonin and volcano islands.