So you returned to the Mothership in the end :)
If you want to unlock a very different ending, try going back to an island where you've already set a data collector in a previous run (the dots are purple) and talk back to the NPC there. It's more interesting if you had talked to the NPC the first time you met him, but it's not mandatory. You can do that anytime /any run before you set the last data collector.
The discovery of what is happening to the islets and their people after you've set a data collector will trigger an event during your way back to the hub after you've set the final data collector ;)
(additionally it should unlock slightly different dialogues in the hub inbetween your runs everytime you visit a purple-dot island and talk to an NPC there)
Tip: Remember to use the save function with Tab to be able to load your game at a certain point, if you're not sure what to do