Base 51 was, in the past, Headquarters for the Highlander Army. It housed millions of soldiers and was used to create weapons, tanks and mechs. It was also used to house the soldiers and develop technology for the Highlander Army.
It was infested with an alien race, and when the Alien Queen was discovered to be there, the Highlander Army pulled out and started a new base.
Base 51 in regards to other armies
Aside of the aliens, no army dared attack the base before when it was in possesion of the Highlander Army. During the second war, the Mercenary Army had been beaten in combat and RFZ let John and his Mercenaries stay there until they recovered and were able to fight again.