The ending you get depends on how many parts you get:

Bad: if you fail to collect the 25 REQUIRED parts of Olimar's ship, he will be stranded forever and become a pikmin.
Normal: If you get the REQUIRED parts of Olimar's ship, he will leave the planet for home.
Great: After you collect the secret safe Olimar will return the planet happy that his ship was repared %100 and there is a little surprise at the end.