It was nice having you join last night Flybrione.
The main objective of the War missions is to destroy the Enemy HQ. The 2nd way of completing the missions is to eliminate all the Enemy hounds. There is always 1 enemy HOUND for every squad member that deploys. So if we have a 5 man squad then there will be 5 enemy HOUNDS to destroy along with whatever other weapons they have, Quad-Leg Spider, 2 leg machine gunners, turrets, tanks , human soldiers. You have to capture COMBAS towers to be able to communicate with the other squadmates. If you wander into the dark area of the map then you will not have any communication abilities until you capture another Combas, get back in range or a Commander gets within your range.
There flags on the map which indicates what country has the majority control of that each region. Regions break down into 3 or 4 battlefields which inturn have individual flags. All nations have a military presence on any battle field but how big is determined by how much control each nation has over that particular battlefield. Every battlefield has color bars that show the total capture points needed to overpower the area and how much each nation has at the point of deployment. Red is for Morskoj, Blue is for Tarakia and Yellow is for Sal Kar. When you enter an area that your country has no power in then you will little to no additional help other than your squad but will encounter a heavy enemy presence. now when you have some to major control of an area you will have several human troops, turrets , bi-peds, that will assist you in defending your HQ.
I hope that helps out and if I may have left something out or wrong please let me know.