Unlike most other mutants that were playable in TMNT Legends, Kirby only appears in his mutant form here - likely as his human incarnation would have little-to-no combat techniques. As this is Dr. O'Neil's sole appearance in a video game, he is only ever shown as a mutant and does not return to human form in this mini-continuity.
TMNT Legends bio
More feral than most mutants, Kirby Bat is non-verbal and doesn't retain much of his human personality. Luckily, Kirby Bat recognizes April and does not harm her. He is calm when she is calm and angry when she is angry.