To change color to dark navy or black you must be a bad boy! Start by kicking all vending machines (many times), kicking animals, kicking the can in Apple Market into the bakery for 1,000 Zenny, not repairing damaged buildings in the City Hall battle, let the bombs explode in the "Bombs in the City" subquest, and by shooting the police car and keeping the "trunk of cash" in the sub-quest when the Pirates rob the bank (you get the bank robbery sub-quest by watching TV in the Flutter after defeating Bruno, the Pirates last robot). When you finally change color (it doesn't take long) it looks really cool!