After you defeat the computer (Shinatama), you are faced with a choice -- kill Commander Griffin or not. Your choice will significantly effect the ending Boss fight. Should you decide to shoot him, you just made things harder on your self. At the final battle you will face your brother after he transforms into a monster. If you do not kill him, the last battle will be slightly easier This time, your brother will approach you with two of his troops and will not transform. Do not worry about the troops, your old "friends" from the TCTF will help you, as well as Commander Griffin, leaving you to face your brother. With either choice, the ending sequence remains the same.