You have a Commander who is your in game representation. The Commander is both a powerful military unit and can also create buildings. If the Commander is lost, you lose the game. Buildings, once created, can be of use in several ways. They may provide radar to allow you to spot enemy units, generate power or mine metal, or build other units.
Units come in four flavors.
K-bots, or infantry, mechanized units, naval units, and air units. Each of these are created by different factories. Some buildings can only be created by specialized building units. These include the higher level factories and the more impressive defensive structures. The object of a mission is typically to eliminate the entire enemy force, but it may be to capture a structure or to defend a position.