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In Mothership Zeta, an alien mothership abducts the Lone Wanderer, making the whole add-on take place onboard the alien ship in orbit around Earth.

Aboard the Mothership, the quest line is not completely linear and features some exploration. The Lone Wanderer will walk outside the ship into space and meet other abductees whom the aliens have captured over time.

The player character is able to return to the ship and use it as a "home-base" of sorts once the main quest is completed, although most of the ship will become inaccessible.