The TL;DR of the situation: Yuji Naka engaged in insider trading during his time working for Square-Enix by gaining early knowledge of a Dragon Quest mobile project in the works and bought shares in the company just before the announcement, which is a no-no in the business world as "insider trading" involves employees for a company gaming the system in a way that's deemed unfair by average investors. Naka wasn't the only Square-Enix employee who got arrested for this situation, but no doubt he's the one who is the most noteworthy in this situation given his legacy, and how he's also been very vocal over the past year alleging that his now former employer Square-Enix supposedly sabotaged his latest project, the highly maligned Balan Wonderworld.
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