This section of the guide to Destroy All Humans explains how to go back to the mothership.
Return to the ship
You can return to the ship at any time, no matter if you're exploring the world or doing a story mission. Remember, however, that the may not be saved in the meantime, so going back tot he ship poses some risk of losing progress.
To get back on the ship, you just have to pause the game. You will have a few choices there. One of them is return to the ship - we highlighted this option in the screen above.
What can you do on the ship?
The mothership is your base of operations. You can fast travel to locations, upgrade your weapons, or repeat missions.