Tendou Jigoku Arc
After the Ura Butou Satsujin, when Mori Kouran has finally revealed his true intentions behind the tournament and the Uruha was dismantled, Joker is one of the remaining few original Uruha Jyushinshuu members, together with Neon and Raiha, who remained loyal to Kurei. Kurei named themselves the Uruha Hokage.
When Recca and company learned of Mori's plan to acquire the ultimate madougu, the Tendou Jigoku, Joker showed them how to enter the sealed lands where the Tendou Jigoku resides. When they entered, Joker remained outside and waited for Kurei to show up. He guided him through the sealed lands to the place where the Tendou Jigoku is in order to face Mori. When Mori fled the battle scene, the Ura Hokage and the Hokage parted ways as well.
In SODOM, at the final stages of defeating Mori and the Tendou Jigoku, in Hokage's final mission, Hell or Heaven, Joker went and searched out Koganei in hopes that they'll finish up their match which they started during the Ura Butou Satsujin. In enters Ura Uruha Shishiten's Kirito, the girl who doesn't know her real age and suffers from multiple personality, and her creature, Shiguma. Joker and Koganei teamed up in order to defeat both Kirito and Shiguma. After defeating them, Kadotsu, which was earlier burned by Kurei and thought to be dead arrived. Joker intending to fight Kadotsu told Koganei to go ahead. As Joker was getting ready to strike his final blow, Kadotsu pierced him with his spear straight through Joker's body. Joker striked back, concentrated his Taishaku Kaiten's gravitational power and opened a dimensional black hole that sucked both him and Kadotsu. This would be the last time that we see Joker.
As to the thought of him dead or not, Anzai has left that open. Yeah, he could have died in the black hole with a wound to the torso like that. But then a lot of people are saying he's pretty much alive but in another world or dimension, this being the MÄR universe, in the person of Nanashi, a character having similar physical characteristics as our lovable Joker. In the Recca universe though, he's gone, never to be seen again. Kirito being the lone witness and saying that both Kadotsu and the guy with the Kansai accent, this being Joker, just vanished and Kurei's reaction are proof enough that he's gone. Alive or dead, it's up to you.