This mission is really simple, when you get right down to it. You begin without a refinery, so make an emissary to build a triad of refineries to the west (sell one). Create anti-air defenses for that location to protect it from Scrin air attacks. Use the remainder of your money to make plenty of stealth tanks, avatars and rocket squads. When you've made a sizable army, head northwest and kill the Scrin there, which are not too challenging. Use lots of rocket squads to garrison the buildings along the path that the civilian transports are taking.
Scrin aircraft will eventually attack, making your rocket squads infinitely useful. They will go up in rank quickly, as well, and punish the Scrin aircraft that try to harass the transports. Use whatever other units you have to help protect the GDI base. Eventually, Kane himself will return and order the GDI base destroyed with a nuke. Build a temple of Nod and use it on the base to satisfy the secondary conditions, then finish off the base with your forces.