The Japanese campaign focuses on the unification of Japan, which was also a scenario in Age of Empires II: The Conquerors, the establishment of the Shogunate, and a young general named Sakuma Kichiro.
The campaign begins when Kichiro meets up with Daimyo Torii Mototada at the siege of Osaka to capture the 5-year-old heir of Toyotomi Hideyoshi. Kichiro and Mototada ally with the local villagers and storm the castle. Next, they move to the north-east of Honshu to destroy any villages that might support Tokugawa's enemy Uesugi Kagekatsu and defeat Uesugi's army. After the victory, in which they suffer heavy losses, Mototada learns that Shogun Tokugawa's main enemy, Ishida Mitsunari, is threatening Mototada's estate at Fushimi, forcing Mototada to return there. Meanwhile, Kichiro marches his exhausted army west again to take control of the Tokaido Road trade route. In the aftermath of the battle there, Kichiro learns from a defeated samurai that it was Tokugawa who destroyed his home when he was a baby and murdered his parents. Kichiro, true to the samurai code, remains loyal to Tokugawa and joins Mototada at Fushimi. Here, Mototada confirms the defeated samurai's story. During the ensuing battle, Kichiro escorts the non-combatants to safety but is forced to leave Mototada to fight alone. As the enemy breaches the final defenses, Mototada commits seppuku (ritualistic suicide for the samurai), detailing in his last statement the importance of loyalty. Kichiro joins Tokugawa at Sekigahara. After the Battle of Sekigahara ends in victory for Tokugawa, Kichiro finally changes his mind, abandons his loyalty to his master, and rides away through the war-torn battlefield, forsaking his honor and shaming his family name for generations.
- The flag used by all enemies of the Act I: Japan campaign appears to be a combination of the emblem (mon) of the Toyotomi clan and the emblem of the Uesugi clan.
- Historically speaking, the campaign is considered out of order, as the battle of Osaka is considered to be the final battle that brought a decisive end to the Sengoku era with the death of Toyotomi's son Hideyori. The correct chronological order would be Uprising! (which likely drew inspiration from the Siege of Shiroshi), followed by Clearing the Road, then Last Stand at Fushimi before the Battle of Sekigahara and finally the Siege of Osaka)
- It makes no sense for this flag to be used by all enemies of the Act I: Japan campaign, since the Toyotomi and Uesugi clans are the enemies in the The Siege of Osaka and Uprising! scenarios, respectively, with the other enemy being the Western Army of Ishida (in the Clearing the Road, Last Stand at Fushimi and The Battle of Sekigahara scenarios).
- This flag in the game is the same flag used by the Japanese, but with the colors reversed (yellow background with the black emblem).