In the true ending, after beating Andross's brain, things are looking bad for Fox. But suddenly, the ghost of James McCloud appears to lead Fox's ship to safety, encouraging him all the way. And even later, the team congratulates Fox. Falco even drops the tough guy act and straight-up compliments you.
If you succeed in helping Bill on Katina, or helping Katt on Zoness, they'll come in to help you out on Solar and Sector Z respectively. (Although even if you fail, Bill will show up in Sector X and Katt will appear at Macbeth.)
Similarly, Rob getting the Great Fox to attack some enemies for you in Area 6. Especially so if the previous level you played was Sector Z, where you were the one covering Great Fox. Now it's returning the favor.