Akira was the lead designer and developer of his "game worlds". Kunai was the lead character of his last created game world (while the "Zero the dragonborn" was from his younger days).
Kunai was controlled by Akira early in the development and testing (think of it as devs testing game mechanics before creating automated game routines or "AI" to execute in-game abilities). You can also think of it as devs (self-)inserting themselves into NPCs into the game as easter eggs. So Kunai "never" lost Akira's soul - but that Akira imbued a part of himself into Kunai as the creator.