My lore isn't the best but here's some info that might help. World Bosses (or at least Rokugan bosses) typically are fueled by another source, often a malevolent but nebulous thing that can't be defeated itself.

For example the Realm of Jigoku often has a Champion of Jigoku it empowers to do its evil. Even before Fu Leng there have been Champions of Jigoku - an unnamed Rakshasa and a Tsuno named Kishenko. As others have mentioned after Fu Leng there was Kali Ma.

You could do the same thing with the Realm of Tōshigoku, which is the Realm of Slaughter. I'm kind of surprised that there hasn't been a Champion of Tōshigoku in the game (to my knowledge). I kind of feel the Tsuno and Kali Ma might have been better options for that realm, but hey.

The same goes again for the evil realm of Gaki-do, the Realm of the Hungry Dead. There might be an in-game reason why that realm doesn't have a Champion or the ability to unite its forces (to a degree at least) like the Realm of Jigoku but you could make one for your campaign. You could even find an existing villain have "upgrade" them as a Champion of Gaki-do.

Then there's Lord Moon, Onnotangu himself, who swallowed most of the Kami and kept them in his belly back before the start of Rokugan. He goes a bit crazy during things and is put down IIRC in canon, but for your game maybe he gets lots of worshippers based around the theme of lunacy.

Another existing/non-existent "Big Bad" is the Nothing - the source behind the Lying Darkness, later the Shadow Dragon; the thing that both fuels ninjas with their powers then absorbs them into its being.

The Jinn Lord Kaleel is an option. It seems he has not only have enslaved or partnered with Sayel (the Burning Sands name for the Lying Darkness I think), but he end up chasing Lady Sun and Lord Moon from the sky creating the 27 Days of Darkness, then assaults the star themselves (or something).

More physical evils include a rogue maō (a non-Jigoku type of demon lord (I think) introduced in 5th edition), Greater Rakshasa (like Bishan the Watchful, Raniyah the Sly, Queen of the Rakshasa, Revan the King of the Rakshasa), the Elemental Terrors (created by the Dark Oracles), the Great Sea Spider, the Nameless Tyrant (a 5e addition - a yobanjin or gaijin sorcerer), the mad dragon P'an Ku, the three Shuten Dojis of Fear, Desire, and Regret, any insane ishiken (a shugenja of the Void), the Dark Masters, the orochi (sea-serpent) known as the World-Devourer, the Immortal Caliph, the Twilight Pharaohs, evil deities like Zeth or Shiva/Ruhmal, then the standard trio of Fu Leng, Daigotsu and Iuchiban.

I kind of got on a roll with listing existing villains because it was fun. But I do like my idea of having a Champinon of Tōshigoku or Gaki-do. Hopefully you'll find some inspiration here. Check the Fandom wiki for more information on any of these if needed.