Naka joined Sega in 1984 and worked on games including Girl's Garden (1985) and Phantasy Star II (1989).

He was the lead programmer of the original Sonic games on the Mega Drive in the early 1990s, which greatly increased Sega's market share.

He joined Square Enix to direct the platform game Balan Wonderworld (2021), which reunited him with Sonic co-creator Naoto Ohshima.

Examples of this include the 3D dungeons of Phantasy Star and ports of Space Harrier and OutRun, which ran on powerful arcade hardware.

[7] During a visit to the 1988 Amusement Machines Show, Naka was impressed by the ability to move diagonally on slopes in a demonstration of Capcom's game Ghouls 'n Ghosts.

[8] Sprite-scaling was still a technique that Naka wanted to improve his skill on with a game called Metal Lancer, but it was cancelled halfway through development.

[9] Of Naka's numerous development plans, "a game to beat Super Mario", caught a superior's attention.

Naka created a prototype platform game that involved a fast-moving character rolling in a ball through a long winding tube.

[20] Originally, Naka wanted to make Sonic 3 a 3D game, with the SVP chip that was also used to port Virtua Racing to the Genesis.

[7] With Naka's return, Sonic Team was officially formed as a brand,[23][24] and began work on a new intellectual property,[22] Nights into Dreams (1996), for Sega's 32-bit Saturn console.

Reportedly, Naka contributed to the cancellation by refusing to let STI use the Nights game engine and threatening to quit.

[29] While Sonic Adventure was in development for the Saturn, Naka was part of the "Dream Team Meetings" which involved talking about plans of what eventually became the Dreamcast as early as 1996.

According to the producer Mark Subotnick, Naka told his team in Japanese which parts they would take to incorporate in Sonic games and suggested firing all but one of the engineers.

However, the other Sega development studios were preoccupied with their own demanding projects such as Sakura Wars series and Jet Set Radio (2000).

In addition to their inexperience, Naka and his team saw the creation of an online game for Japan, a nation of console gamers, as a serious challenge, akin to creating a new genre.

This was further complicated by the perception of online games in the late 1990s having boring visuals and the per-minute fee for dial-up internet in Japan.

[33] Naka split his team into three groups, all serving different purposes, before rejoining to develop Phantasy Star Online (2001).

Two groups were focused on discovering the limits of the Dreamcast's capabilities, specifically in terms of graphical fidelity and the possibilities of online play on the system.

[33] Additionally, it was the only game directed by Naka at Sega as he would move on to become a producer, overseeing output from Sonic Team.

[39] After Sega left the hardware market, Sonic Team began developing for consoles by other manufacturers;[40] Naka became fond of the Nintendo GameCube.

[42] Naka also explained that the video game industry was young, leading to quick promotions; he felt his senior position had given him less time to be close to development.

[51] In 2018, Naka joined Square Enix to form the subsidiary developer Balan Company, which aimed to facilitate collaboration between internal and external staff.

A key staff member at Arzest was Naoto Ohshima, a former Sega artist who created the designs for Sonic the Hedgehog and Doctor Eggman.

[57] In July, Naka tweeted a photo of the Nights team with Ohshima's face blacked out, and expressed his anger over Balan Wonderworld.

[58] 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.

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.

[61][59][60] On December 7, Naka was arrested again, accused of having purchased 144.7 million yen of shares of the developer ATeam before their game Final Fantasy VII: The First Soldier was announced.

In April 2024, he ended his social media hiatus to respond to the news that Yu Miyake, Dragon Quest's executive producer, was being reassigned to Square Enix's mobile division by accusing him of lying during the trial.

[68] In April 2022, Naka participated in the first round of the Elise Super Tech competition at the Mobility Resort Motegi circuit, finishing seventh place.