Each faction has its own choice of two available missions. Bauhaus, for example, has the 240 mm Tapered Bore Helga Cannon and the V-120 Delivered Donnerschlag AV Pod. Therefore, as long as the army fits the criteria to have a Force Commander (six squads, three officers and one Force Commander) and a Forward Observer (F.O.) model, then one of either mission may be called into play each turn, for no additional cost (meeting the requirements is the cost).
The sentence, "...army's Force Commander, along with their cost" is misleading.
Does that clear it up?