Taking this bit by bit.
1. The Tournament of the Kami.
What if Fu Leng felt among his brothers instead of far away? And then won the Tournament of the Kami against a wounded Hantei after his fight with Akodo? What Empire would the ninth Kami have forged?
Interesting premise. Without Fu Leng cratering through to Jigoku you'd need some other event to introduce Jigoku to the early Empire. You could have one of the non-human empires that dwell there find a way in maybe? Or the Tsuno. You could even have the early Kolat ally with the Lying Darkness, or the nonhumans (maybe both?) in a bid to run these Kami and their followers out of Rokugan. You still get a huge First War against the forces of evil, but with different players and different stakes.
I could see the Crab Clan maybe going into an offensive role here. Instead of protecting against a Shadowlands that doesn't exist, they are the conquerors spreading Rokugan into the territories of the non-humans, maybe with help from Akodo and his Lion Clan. Hantei would need to form his own clan as well, and it would need it's own themes. Perhaps they would take the Mantis's role as seafarers?
2. The failure of the Thunders
The Seven Thunders failed to stop Fu Leng and his Jigoku-fueled army. He entered Rokugan and slayed Hantei on his throne, taking his rightful place as the leader of Man. How would that shape the future of Rokugan?
The immediate problem I see here is, what keeps Fu Leng from just slaughtering all the humans? In the Thousand Years of Darkness setting there was Kachiko planting the ideas of ruling instead of killing. What restrains him here? And what keeps Hantei and the other Kami from deciding that Shinsei's plan was stupid and they're going to go handle their wayward brother themselves? How does Fu Leng deal with all his siblings ganging up on him?
That said, a lot of the cultural issues that came up in the first thread aren't as big a deal here. The cultural patterns and traditions aren't set in stone yet. The clans are just forming and Rokugan is already in a period of upheaval since the Kami came down and rearranged everything. So you'd have Kami loyalists who tried to hold to their ways and you'd have those tribes that hadn't been won over or stomped flat that might just shrug and adjust to a new world of taint and monsters. Or at least, be willing to find a way to prosper in it with a lot less fuss than in later eras. The Kami loyalists might even be the ones who flee the Empire or form something like the Kolat.
3. Isawa's Last Wish
After Fu Leng's defeat, the Isawas and the Asakos fought for the possession of Isawa's unfinished creation. After decades of bickering, one side decided to use maho to shift the balace of the conflict in their favor, with catastrophic consequences. Through taint, the wish was completed, but what was supposed to be a pure soul was twisted in the process. Using this newfound power, the most powerful nemuranai ever created set forth to conquer the whole Rokugan. Using is own reality warping talent and the power of Jigoku, he took form and made the world his own, killing Hantei Genji and taking the throne for himself. Since then, Rokugan lives under the rule of an immortal magical artifact corrupted by the taint.
I like the idea, but I'd need more details. What is this artifact like? What makes it such a terror? The traditions of Rokugan aren't as set in stone yet, but they are more defined in the time of the Thunders, and I think there would be much greater resistance. I could also picture shugenja becoming hunted people. Not only so they don't prove a threat to the Wish, but also because people would remember it was shugenja who made their immortal tyrant.
4. Akuma's conquest
After Isawa Akuma summons the Oni now know as Akuma no Oni, the latter leads the army of the shadowlands into Rokugan, destroying everything in his path. The world is in ruins and the handful of survivors fight everyday against the harsh elements, hunger, corruption, and the hordes of goblins, undead and onis rampaging the land. It's the end of the world as we know it, but somehow, some samurai live to fight another day and might restore Rokugan to its former glory and get rid of the taint.
It sounds like the Thousand Years of Darkness. What would be the difference?
5. Five Nights of Change
The Chudas not only survive the Five Nights of Shame, but manage to destroy the Phoenix Clan with their power. Using the now undead bodies of their neighbours, they set off to deal with the rest of Rokugan. After a few years of bloodsheds, Chuda Tamihei now sits on the throne and controls an army of undead to ensure the loyalty of the rest of Rokugan. All magical research is now aimed at unlocking new heights of power.
That'd have to be some massive bloodshed. By this point traditions have hardened and Chuda Tamihei would spend the rest of his/her life stamping out rebellions. I imagine the Crab and the Lion would join together to be one massive army against them. The Scorpion and the Imperial Families would be sabotaging with all they've got, same with the Crane.
I think the challenge here is figuring out how the Chudas survive with a whole Empire against them. They'd need allies from somewhere and it occurs to me that they might find them with the khadi. Possibly they could hold Rokugan with a combination of Jigoku power, maho, gaijin sorcery, and maybe troops from a conquered Medinaat al-Salaam and Yobanjin tribes. It would make the return of the Unicorn a much bigger event though, especially for beleaguered rebels.
6. Touch of the Darkness
The Nothing made its way into the highest spheres of Rokugan and then unleash its full might, corrupting and absorbing most of the world. Now, the survivors follow a faceless emperor and struggle to maintain their own identity in a world of servitude. Not sure how this could go, but I felt it was important to include it.
Maybe set it during the War Against the Darkness. Rokugan survives the Second Day of Thunder only to have most of it's cosmology consumed by the Nothing. Maybe Mirumoto Hitomi kills Goju Adorai and becomes the avatar of the Nothing, reigning over Rokugan as it's Empress. A mind-controlling tyrant with the power of the Nothing and the Obsidian Hand. Tengoku and Yomi are gone, but survivors from both realms have set up in what's left of Yume-do, trying to form a resistance movement. Ningen-do is on it's own, and while a resistance movement has sprung up in Rokugan, a lot of people have fled the country. Probably a lot of people joined the Mantis and fled to the Ivory Kingdoms, or the Unicorn and fled to Medinaat al-Salaam. The best hope for Rokugan here might be an invasion from the Yodotai.
Although, there is still the Jade Hand out there, waiting for a hero...or maybe not for maximum darkness.
7.Rise of Iuchiban
The dark Otomo Iuchiban unleash his army of bloodspeaker to take control of the Empire. He succeeds and sit on the throne as the rightful Hantei ruler, but blood magic is now an accepted practice.
I'm thinking that's doable, but he might have taken more time than he did in canon. Iuchiban's problem has always been acting too soon. Maybe here he eliminated the two magistrates and built a giant army not just of Rokugani, but gaijin corpses too. Again, I'm thinking he might want to get some outside help to hold his Empire against the massive resistance he's bound to face. It occurs to me that this idea might be combined with your next one.
8. The return of Hawthorne
The undead Garen Hawthorne returns to Rokugan with a fleet so great the Rokugani are unable to stop him. He kills the Emperor and manages to quell any rebellion with his undead minions and the power of the taint. He edicts new laws that radically changes Rokugan's culture, like the legalization of Firearms, and accelerates the production of natural ressources to incredible heights, shipping most of them for a profit to distant lands. Think Iron Rokugan with a western undead madman who created Shourido in charge.
Iuchiban might have recruited Hawthorne's naval forces to help him conquer Rokugan, just as he recruited aid from the khadi and learned their secrets. A team-up between them could create all kinds of tensions, especially between Hawthorne, Iuchiban, and an ambitious Yajinden. You'd still get the introduction of gaijin technology and have it forced on the Empire along with maho and the undead. And it'd give Iuchiban a force to stand against the Clans and internal resistance.
9. The Dark Emperor
The Spider Clan wins the Race for the Throne and Daigotsu Kanpeki is named Emperor by the Voice of the Sun and Moon. The Dark Lord himself has the backing of Heavens to rule!
I'd imagine the Empire would be struggling to cope with all the implications of Daigotsu on the throne. Though he'd get a chance to prove himself a few years later when Kali-Ma came through. I'd imagine that he and Shahai might die securing the victory, leaving a regent to raise his infant son. You'd get a period where the Empire was rebuilding while the schemers plotted to take the throne, or at least manipulate the heir. The Colonies would probably be a secondary concern. Something the Regent orders to get some of the clans out of the Empire and weaken them. So the Colonies might not be as developed. I'd imagine Kanpeki is going to have to establish himself quickly and decisively and the setting would be ripe with possibilities for intrigue and character development.
10. P'an Ku's Madness
The Empress Iweko falls prey to the madness of P'an Ku and an evil duplicate version of herself is created. Rokugan falls into civil war, with both sides siding with a version of Iweko. Madness, destruction and mayhem ensues.
Interesting. What about her sons? Would either of them step up to try and lead during the crisis?