L5R Timeline
Sometimes information conflicts. Sometimes there is an obvious solution - the Unicorn Clan would obviously not be present during a battle when they hadn't yet returned to Rokugan. Other times, information is directly contradictory. Obviously, since we're going over 'classic' Rokugan, information gleaned post-Clan War is considered to be more suspect. In addition, I consider Bearers of Jade to be one of the finest RPG supplements ever written, so information in that book will especially supersede information from other sources.
Prehistory
Before the fall of the Kami, before the rise of man, there were others. The oldest civilization believed to have existed in the land now known as Rokugan was that of the Naga. A race of mystical, pacifistic serpent-men, the Naga carved a great civilization that spanned the far western reaches of the modern Empire. Their history was marked by conflict just as any other history, but following their own struggles for supremacy and a war with the mysterious Ashalan from across the desert, the Naga established a peaceful and philosophical society that reigned for many centuries.
Eventually the Naga entered an enchanted slumber in order to preserve their dying race and combat some unknown future enemy. In their wake, other civilizations emerged. The greatest was that of the Nezumi, also known as Ratlings by modern Rokugani. The Nezumi profess to have had a vast empire of their own, one in which they conquered the kingdom of the ogres that dwelled where the Shadowlands are today. Although many Samurai refuse to believe that the abominable ogres that served Fu Leng night ever have been civilized creatures, there is some small amount of evidence to support the Nezumi's assertion. Whatever the truth may be, both the civilization of Nezumi and that of the ogres was destroyed with Fu Leng's fall from heaven over a millennium ago, although both races continue to exist to this day.
At least one other civilization existed prior to that of mankind: the trolls. Whether created or merely corrupted by Fu Leng, the trolls nevertheless managed to forge a considerable kingdom throughout the Shadowlands. This kingdom bowed to the rule of the trolls, survived the reign of the Nezumi, was incorporated into the dominion of Fu Leng, and finally was shattered during the rule of Hida Osano-Wo, child of Hida himself, who led the Crab Clan in a vicious war against the trolls. Remnants of their civilization may still exist, however, such as the dark city Volturnum.