The Motherships are structures built by the Espheni.
They are home bases of the loyal Skitters, Mechs, Mega Mechs, and Overlords. They are heavily guarded and fortified. There are thousands of these structures in major cites around the world.("Live and Learn")
It was revealed by Cochise that they are defensive structures designed to prevent hostile ships from entering a planet's atmosphere through activation of a defense Grid.(On Thin Ice) He also later revealed that the ships, when activated, will create an energy grid capable of blocking ships from entering the atmosphere, prolonged use will irradiate the planet and destroy all life on Earth in 3 months. The Espheni and their harnessed subjects have been genetically engineered to withstand this radiation.(The Pickett Line)
In Prisoner of War the Harnessed Children where gathering steel and scrap metal to help with the building of the Skitter "Mothership".
Tom Mason observes that the four protruding 'arms' resemble that of an aircraft carrier. Despite its alien nature Weaver noticed that the craftsmanship was very basic and could be easily taken out with the right amount of explosives.
In Eight Hours, this was proven true when a large number of attack ships retreating and entering through these arms. Tom Mason fires a mech-metal RPG at a ship attempting to dock. The ship is hit and crashes in to the arm, causing significant damage and resulting in a chain of explosions running down that particular arm.
Cochise, informs Tom that they will have to destroy on of the Motherships in order to deactivate the Grid. The Volm that were able to land near Charleston were working on designing a cannon that would be able to destroy these motherships so that the Volm can enter the fight in full force.
While Tom was being held in Boston, the grid was activated; however, sometime later the Boston Mothership was destroyed, disrupting the grid and allowing a gigantic Volm ship to land on Earth, opening a second battlefront against the Espheni.(Strange Brew)