During the Yuuzhan Vong invasion, in the New Jedi Order saga, Kyle helped develop strategies against the invaders, freed the human captives of the Imperial Remnant world Ord Sedra. Near the end of the war, the living planet Zonama Sekot agreed to help the Republic and Kyle was one of several Jedi Knights bonded to seed-partners and provided with Sekotan starships in the final battle.
Kyle heard a rumor that the Sith Order still existed. Due to his experiences on Drommund Kaas, Kyle investigated after the invasion, following clues from Ord Sedra in the Clacis Sector to Yaga Minor, resulting in the Cloak of the Sith. During the mission, Kyle was captured by the dark Jedi Daye Azur-Jamin, who presumably attempted to turn Kyle back to the dark side. After a successful rescue mission led by Jan Ors and Jaden Korr, Kyle revealed all that he knew about the new threat. A force-sensitive Yuuzhan Vong is causing havoc in the galaxy, and it's apparent that an even more powerful threat looms on the horizon.