Here are the mini-settings involved in the two Imperial Histories books:
(note, settings tagged with ** are either canon timelines that have NEVER been discussed or mentioned before, or alternate/future timelines)
** The Five Rings Heresy - A monk comes up with the idea that since there's five rings,. there should only be five clans, and proposes that the Crane and Scorpion merge for greater harmony in the Empire. The scary thing is, he's popular enough with the Emperor that despite the Crane and Scorpion both being, um, less then enthused about it (I think both Clans are equally disgusted by the idea) that it comes VERY close to happening. Would be very good for courtier characters.
** The Great Famine - Years of Bad Harvests have put all the Clans in a bad position. There's no food to trade, so what do the Great Clans do to feed their peasants, without causing all out war? And what happens when the Peasants start rising up when they think the samurai are living the life while they can't even keep the food they grow to stay alive.. (it's an official time.line, but never was mentioned before, so I tagged it)
The Rise of The Gozoku: Basically, a bunch of powerful clans decide the Empire would be much better if the Emperor/Empress was a figurehead (after all, how can just one man or woman rule such a vast land), and instead the true reigns of power was in the hands of a select group of Clan leaders
Prelude to the Scorpion Clan Coup: If you played previous editions, you know what this timeline is like. It's the base setting for I believe 1st edition. The leader of the Scorpion Clan receives a horrifying prophecy "The Last Hantei will bring doom to Rokugan".. how far will they go to prevent this future from happening?
The Dawn of the Empire: What happens to a tribal world when the seven Kami fall from the Heavens? (With some neat notes on playing alternate histories where one of the OTHER Kami won the original Celestial Tournament)
** Heroes of Rokugan: Based off the "Living L5R" campaign from conventions and the like, the Toturi dynasty never fell, and it's several centuries in the future
The Clan War: Post the Scorpion Clan Coup, the Empire is falling apart.. the Crab have allied with their ancient enemies in the Shadowlands in an attempt to seize the throne from the ailing Hantei XXXIX. This brings about the return of Fu Leng (who possesses the Emperor), and war breaks out amongst the Clans. The ronin Toturi attempts to rally an army to protect the Empire, but this leads to the Second Day of Thunder.
** A Thousand Years of Darkness: The Second Day of Thunder is over. But in this alternate timeline, the Seven Thunders fell before Fu Leng, and Fu Leng now rules Rokugan directly. He's broken most of the resistance against his rule, but here and there, small packs of samurai bravely try to push back.
The Hidden Emperor: The spirit of Nothing has kidnapped and corrupted the emperor, and is trying to unmake all reality. Without the Emperor to guide Rokugan, is all lost?
The War of Spirits: One of the cruelest Emperors in all of Rokugan's history has returned from the War of Spirits. He claims the Throne belongs to his family, and Toturi (who committed seppuku to not let the spirit of Nothing corrupt him and thus the Emperor) is an usurper. This of course, means war.
Battle of White Stag: Rokugan is under attack from Gaijin with strange gunpowder weapons, who seek to conquer the Empire!
** The Togashi Dynasty (an offshoot of Dawn of the Kami).. The Immortal Togashi wins the Celestial tournament.. how does the empire differ when an immortal Dragon is on the throne?
Reign of the Shining Prince: L5R in the age of the "Shining Prince, the son of Hantei, Hantei Genji.
** The Iron Empire: Kinda a steampunkish L5R, as it explores the "modernization" of Rokugan, with Railroads and the like.. but with all these new fangled ideas, what room is there for the ideals and skills of the samurai?
The Reign of the Steel Chrysanthemum: Remember that vicious, evil Emperor I mentioned above? this is when he reigned, and controlled Rokugan in the grip of Terror and hatred.
The Eight Century Crisis: One crisis after another (Bloodspeakers, war, famine) beset the empire. Will the series of blows be enough to topple the Empire?
** The Shattered Empire: Six of the Seven Thunders from the Second Day of Thunder lie dead. The Seventh has been touched by Madness and the spirit of Nothing. With no Emperor to keep the peace, the victory won on the Day of Thunder may not mean much as all the clans squabble and fight over who the Emperor should be (and in somecases, even if there SHOULD be an emperor)
The Four Winds: The Emperor is dead, without having named an heir. His four offspring all have a valid claim to the throne. Who will claim the Throne?
** The Shadowed Throne: The Glorious General, Toturi Tsudao has won the War of the Four Winds and is Empress Toturi II.. but is she the right person to lead the Empire going forward?
The Destroyer War: Kali-Ma and the Destroyers threaten to overwhelm Rokugan.. what are the powers of those who serve the Kami worth against the avatars of Foreign Gods?
The Colonies: In the wake of the Destroyer War, the former lands of the Burning Sands lie vacant. Samurai from Rokugan claim this territory, and Rokugan grows, but so far from the Empress and the Empire, how will the Colonies fare?
The Emerald Stars: Rokugan has taken over the world. Many worlds in fact.. yup, you guessed it, this is Rokugan IN SPACE, hundreds of years in the future.