From Command and Conquer Wiki
The Sub pen was a Soviet structure that was used to construct, repair and maintain their submarine fleets. The internal equipment was shielded by a concrete, tetragonal triangle shaped dome built on eight supports embedded in the seabed. They also usually held data about the locations of all subs in active duty in the surrounding area, making them high priorty targets for spies in operations that involve naval engagements. If a spy infiltrated the building, the data could be accessed and a single sonar pulse discharged.
The pen allowed for Victor submarines and their missile variants to be constructed as well as hover transports. While the Soviets were defeated, with the development of submarine warfare, the submarine pen was designs were not put out of commission.
By the third world war the Soviets replaced their Submarine pens with Naval Shipyards. Yuri, however, continued to use them to construct his Boomer Submarines and transports.
[edit] See Also
Soviet Great World War II Arsenal 
Yuri Great World War III Arsenal 