Dr. Habbitrale appears in the early stages of the game where he is at his hideout placing a mutating gene into the Greema alien species, turning them into vicious monsters. He appears to have a rivalry with Dr. Jumba Jookiba as they are both evil scientists. He gives the word to his mutant Greemas to have Experiment 626 eliminated as he believes that by killing 626, he will be proving himself better than Jumba.
Later on, 626 finds him in his lair. He is the first boss that 626 battles in game. He takes on 626 inside a giant robot but is soon defeated when 626 throws small rockets at the robot. Habbitrale escapes into space inside a giant hamster ball.
He appears again at the end of the game where he's still floating in space.