you have to trigger the factions to give you missions.

the company ask you to take out the navy buildings.
the eden lot ask you to disable the air assets.
the saat lot as yo uto blow up the sub base.

each one give you a nice item.

you use the item ot unlock an resurch bost.
compay give you better weapons
eden armoyr i think?
and then thers soem other boost.

these are all bloble effects bar the saat one.

you then use the emp device to disable all the units defending father and also father.

you shoot up the ships and father defencive turrets
then father him self.

send the emp ship in solo. else yoru own ships wil lbe hit by the emp also.

you win whne father is down.

the faction quests are over kill you dotn need them to win but they make it less painful.

your alone as the comanpy exct was arasted by you in the last mission.