The Maintenance Factory produces the nutrients and energy for all other buildings. This is done by pumping the nutrient liquid through the connecting tube that runs through the city, just like blood in a cardiovascular system. The destruction of this building will be a significant blow to the Aliens and allow us to destroy all remaining structures.
The Maintenance Factory appears to contain a number of sacred Alien structures. We believe that the Alien Dimension is fueled by the structures pictured here. These heart units must be destroyed in order to weaken the remaining structures. Our success here will indeed be a severe blow to the Aliens as exactly half of the Alien Dimension will lie in ruins.
The target structures are easily found and explode easily when shot with Devastator Cannons, though a Vortex Mine is also a sure thing.