Two other former Square Enix employees were also arrested, alleged to have bought 162,000 shares between December 2019 and February 2020 for approximately 47.2 million yen. The Public Prosecutors Office accused him of insider trading Naka bought 10,000 shares of the developer Aiming before its game Dragon Quest Tact was announced to the public.

On November 17, 2022, Naka was arrested by the Tokyo District Public Prosecutors Office and charged with violating the Financial Instruments and Exchange Act of 2006. He posted an image of the NiGHTS into Dreams team with Naoto Oshima seemingly blacked out with marker. On July 5, 2022, Naka posted another thread about discovering in court documents that coworkers at Square Enix had been talking behind his back. Naka stated that his protests were ignored. He stated that he was removed as the director of Balan Wonderworld six months before the game's release following disagreements over the game's stability. On April 28, 2022, Naka revealed in a Twitter thread that he had filed a lawsuit against Square Enix. He posted a fairly vague message concerning his reasons for doing so but stated he may retire. In April 2021, upon the release and commercial failure of Balan Wonderworld, Naka left Square Enix. On July 23, 2020, Balan Wonderworld was revealed as a new 3D platformer from Yuji Naka and Naoto Oshima. The new developer would work with internal and external studios to make games that were more atypical for Square Enix. On July 16, 2020, it was announced that Square Enix had formed the subsidiary developer Balan Company. In January 2018, Naka joined Square Enix. It was built in Unity and his first time creating a game entirely by himself. On December 18, 2021, Naka released the free mobile game Shot2048 through Prope. By 2019, Naka's work with Prope was largely administrative tasks he performed during weekends. Naka left Sega to set up this studio, called Prope.ĭuring his 2018-2021 employment with Square Enix, Prope remained in business with Naka as the only employee. On Mait was announced that Naka would be creating his own independent game studio, with partial financial backing from Sega. Naka would serve as a direct programmer on Sega titles up until NiGHTS into Dreams, when Sonic Team members Tetsu Katano and Takahiro Hamano succeeded him in that regard.

In 1990 he, along with Naoto Oshima and Hirokazu Yasuhara, began to conceive what would become Sonic the Hedgehog, assembling what would later be dubbed Sonic Team, putting his leadership and programming talents into work. Examples of this are Space Harrier II and Phantasy Star II. Yuji Naka's distinction was producing/project managing projects while simultaneously handling the lead programming of them.

His first release was a game for the SG-1000 called Girl's Garden. A 1996 photograph of Yuji Naka and Sonic Team.

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