Star Control: Origins will take place in our little corner of the milky way galaxy. While there are thousands of planets and we expect it to take as long or longer than Star Control 2 to finish the main story, we have many different adventures in mind for the future that will add new aliens, new worlds to explore, new ships, new components for your main ship and so forth.
At the very least, we have 3 major expansions along with about a dozen DLCs that will range from adding new stories all the way down to cosmetic enhancements to your ships and everything in between.
To use a crude example, if Star Control 2 had been called Star Control: Ur-Quan, then what ws called Star Control 3 would have been a DLC for Star Control: Ur-Quan (like DLC: Space Cows...)