Here is what happened in thumbnail:
1. Initial Skirmishes. The Naga fought and destroyed a sizeable portion of the Shadowlands horde on the outskirts of the capital using ranged attacks, their own pearl magic, and tactical guidance provided by Mirumoto Daini.
2. The Elemental Masters fought between themselves in a brutal series of magical battles that removed many of the Phoenix shugenja from the assault on the capitol and killed most of them. In the end Isawa Tsuke was destroyed by Shiba Ujimitsu, the Phoenix daimyo, who died in the conflict. Of the Elemental Masters, only Tadaka lived - (and Kaede, who was and remains missing).
3. The Lion Schism was healed by Toturi, who rode into the battle at the head of an awesome army of ronin and clan samurai. Calling on the Lion to heed the cry "For Rokugan!" he stopped the intra-clan battle and managed to avert the total destruction of his former clan at their own hands.
4. Yoritomo gained recognition as a major clan daimyo from Toturi and the other seven thunders just before they entered Otosan Uchi to face Fu Leng.
5. The Unicorn battle maidens rode down Yogo Junzo's horde, killing the undead creatures he commanded, and Otaku Kamoko killed Junzo herself by trampling him with her mighty steed.
6. The Seven Thunders, Togashi Yokuni, and the Hooded Ronin proceeded into the palace to hunt down Fu Leng and destroy him. Ê 6.a. In the throne room, Togashi Yokuni revealed that he was in fact Togashi, one of the kami who founded the Empire, and brother to Fu Leng. Fu Leng mortally wounded Togashi, but before he died, Mirumoto Hitomi (Dragon Thunder) used the Obsidian Hand to rip open his chest and pull forth the 12th black scroll, which had been hidden within Togashi for a thousand years. In the process, Hitomi consumed much of Togashi's spiritual essence and gained some of his powers.
6.b. Fu Leng laughed to see the 12th Black Scroll, believing that its appearance gave him the victory. When Hitomi opened it, instead of gaining his true and total powers, the Hooded Ronin took great delight in informing Fu Leng that his long imprisonment was now complete, and that the 12th Scroll had given him total control of the possessed body he inhabited - and had made him mortal.
6.c. There was a great battle, many desperate moments, and in the end, Toturi and Hoturi killed Fu Leng with a double strike of their ancestral swords, carrying the day for the forces of light and the Seven Thunders.
7. A whole lot of people died. The known dead include Doji Hoturi, Isawa Tadaka, Isawa Tsuke, Isawa Tomo, and Isawa Uona, Togashi, Yogo Junzo (completely dead), Alhundro Cornejo (unaligned anachronism), most of the Phoenix shugenja, and thousands of other ronin and clan samurai of greater or lesser repute.
In the end, Toturi was named Emperor, the whole Empire began the slow process of rebuilding, and the stage was set for the Jade Edition and the Hidden Emperor story arc, which began at the end of June.