MI added the Mongol invasion campaign and with it several Mogol and Korean (allies) units. The Hojo clan controls all of Japan and the Mongols try to take it from them. Mongols start with a large army invading Japan. They don't construct buildings to add on to their army. Instead they have to loot Japanese provinces and the better they do, the more reinforcements come from the mainland to replace combat losses. The Japanese also get a few new units: naginata cavalry and kensai (one man killing machines).

The only other aspect of the game I recall changing is that the movement rates of the units increased. I remember the feeling that it looked unnaturally fast compared to the movement rates in STW.