The Mothership was a massive vessel of the Furon Navy that was used for battle, exploration, laboratory experiments, or missions.
The Mothership had numerous accessible areas, some of which included the Hangar, the Furon Archives and Orthopox's Lab.
The Mothership was blown to pieces in 1969 when the Soviet Union launched a missile at it. Pox was killed, but not before he downloaded his mind data into a HoloPox Unit.