In 2006, Naka left Sega and had no involvement with the development of anything regards the NiGHTS series since then. He is currently working at Square Enix.
- NiGHTS into Dreams: Lead Producer / Programmer
- Christmas NiGHTS: Producer / Programmer
- NiGHTS into Dreams (Japan exclusive Playstation 2 port): Special Thanks
- Years after leaving Sega, Yuji Naka worked again with NiGHTS' original character designer, Naoto Ohshima, at Square Enix and together, they made a Platformer game called Balan Wonderworld. Fans noticed that the game was inspired by the NiGHTS series.
- Before working for Square Enix, Yuji Naka founded an independent video game company called Prope. There, he developed a game called Rodea the Sky Soldier, which also took inspiration from the NiGHTS series.