The Mothership is a large-scale invasion craft and mobile command center, designed to transport entire armies at at a time.
| Spoiler warning!|
Plot and/or ending details follow.
The Martian Empire dispatched the Mothership from its nearest colony to exact revenge for the JFO's wholesale murder of all Martians on Earth. The USS Destiny encountered the Mothership as it entered the Solar System, and was captured by the Martian craft.
Some time thereafter, the Mothership reached Earth and launched an all-out attack on various cities across the globe. While SEMME fought the Martian forces on the ground, Joe Rosenthal, Danny Wilcox, Rachel, and Howard Lesse penetrated the ship's defenses in the newly-developed Ultra Car and blasted their way through the interior. In the process, they rescued Phil, the Destiny's janitor and last surviving crew member, and eventually destroyed the Mothership entirely.
20 years later, another Mothership arrived at Earth. The human defenders attempted to teleport Bobby Walkerton directly into the heart of the vessel, but miscalculated and sent him into a time portal instead, sparking the events of Joyce and Walky!.