Different Ending Sequence
Upon defeating Andross the hard way, which is after going through Area 6, you will be saved by your father.
When you fly back into space to meet your team, two things will change. First the dialogue of the characters and secondly Fox will look around to symbolize him trying to seek out his father after the escape. He doesn't see him, however, and tells his team mates not to worry when they ask what's bothering him. His father may be gone, but not forgotten.