The Scorpion Clan daimyo, Bayushi Shoju, has come to believe that an ancient prophecy long held by his clan (the Prophesies of Uikku) indicate that the 38th Hantei Emperor will be the source of a consuming evil that will destroy Rokugan.
He acts on these beliefs by killing his liege, the 38th Hantei, and then attempting to hold the Imperial capitol of Otosan Uchi against the massed armies of the other Clans. This defense will be successful if the Crab Clan throw their allegiance behind Shoju.
In the end, Hida Kisada, Crab Clan daimyo, does not support Shoju. The Lion Clan daimyo, Akodo Toturi, kills Shoju in the resulting general melee in and around Otosan Uchi.
[ The next events occur after the end of the Coup, but before the Imperial Edition begins ]
The story branches into several sub-stories at this point, most of which have some final resolution by the release of the 5th expansion, Time of the Void.
The Crane Clan lead a pogrom against the Scorpion Clan in retaliation for the Coup, seeking to destroy them utterly.
At the palace, the son of the dead Emperor is named the 39th Emperor of Rokugan. The son is a vain and churlish man who was spared from the Coup and the attempts of the Scorpion assassins to kill him by unknown plot developments that may be explored in future sets. He is enraged at the Scorpion, and as a part of an elaborate series of revenge-motivated actions, he declares that he will take Bayushi Kachiko, the most beautiful woman in Rokugan, and wife of the recently deceased Shoju, as his new bride, ending Shoju's line.
Akodo Toturi believes this course of action is unwise, and he protests the Emperor's actions. Having been nearly killed earlier by a poison slipped into his sake, thus failing in his duty to protect the 38th Hantei Emperor, combined with the public rebuke of the new Son of Heaven is too much for Hantei the 39th. He orders Toturi stripped of his family name, and he orders all the other Akodo to abandon their names as well, save Akodo Kage, the reversed Master Sensei of the Lion Clan who is above reproach. Further, he refuses Toturi the opportunity to commit seppuku, and instead sends him forth from the capitol a dishonored ronin - the ultimate disgrace.
Somewhere in the Empire, not currently disclosed, Yogo Junzo receives news of the Crane purge and the actions of the new Emperor. He betrays his families thousand-year oath to guard and protect the "black scrolls" - ancient spells used to bind and banish the dark god Fu Leng at the same time the Empire itself was founded. When he opens the scroll he guards, its malevolent powers consume his spirit, and he becomes a puppet in the service of Fu Leng. The opening of the Scroll also unleashes a deadly magical plague that begins to spread through the Empire, killing thousands.
The plague reaches Otosan Uchi, and many members of the Imperial Court are stricken, including the new Emperor and all the remaining Hantei heirs - in fact, the Imperial City is decimated by the plague despite the best efforts of the various shugenja and monks who have arrived to treat its victims.
In the aftermath of the Coup, the purge of the Scorpion, and the terrible sickness sweeping the Empire, the various Clans begin to turn on one another, first in minor skirmishes, then in outright warfare.
Following a thwarted assassination attempt on the Emperor (thwarted, surprisingly enough by Kachiko herself, who is wounded in the process), word is sent to all the Clans that the Emperor is dying, and that he will name as his successor the Clan noble who best exemplifies the code of bushido and the command of the Tao of Shinsei.
Stepping out of the mists of legend and rumor, a strange group of half man, half serpent creatures known as the Naga reappear in Rokugan, though sightings of the creatures are few and far between.
Doji Satsume, Crane Clan Champion and Emerald Champion dies during this time, though the nature and reasons for his death remain unrevealed.