This mission can be very difficult, but not with a working strategy. Your goal is to capture four construction yards (2 GDI, 2 Scrin). If any of them are destroyed, your mission is over. When you begin, send your shadow strike teams to the west while you train saboteurs. Perhaps ten or so. Glide the shadow teams to the western corner, and land near the sentry towers. Use two teams on each tower to destroy it. GDI will ignore you, for now, so long as you don't attack any infantry.
The next order of business, is while your teams are busy taking out the other pair of sentry towers to the northeast near the war factories, you send the Commando, along with the saboteurs, to the base. Use your shadow strike teams to begin your assault on the GDI there, killing all the infantry. When the commando arrives, have her help while the saboteurs capture all the buildings except the four power plants to the south (GDI needs them to hold off the Scrin for now). Capture the refinery while the harvester is docked to capture it as well. Don't forget that you can get a battle base here, too!
When you have the construction yard, start making refineries (one more for each of your bases) while your war factory produces tanks and the barracks train missile squads. Get some more of your super saboteurs over to the base so they can assist in capturing the northern GDI base. Build a fairly large army consisting of at least eight predators, ten missile squads, the Commando, and four to six shadow strike teams. Push to the north, killing anything in sight. When you reach the GDI base ignore the air field's small outpost for now and make your way for the base proper. Focus fire on the sentry towers and eliminate any hostiles, then send in your engineers to capture everything!
With both bases in your control, you are the one who decides when to attack the Scrin because you aren't on the clock. Build a sonic emitter at each of your bases along with plenty of missile squads to hold off walkers (capture with engineers!). Thankfully, the Scrin base isn't that well defended. Make four or more mammoths, ten predators (rail gun upgrade!), and a small horde of missile squads. Use APCs for anti-air and infantry. At the base you started with, make several saboteurs.
Attack first the Scrin base just north of the base you started with. Make sure to send every troop in at once so that the mammoths aren't too far behind. You need their power! Focus fire on any base defenses then send in the saboteurs to capture the drone platform. Capture everything else! If you need reinforcements, it should be safe to do so while you park there. Finally, take the northern Scrin base just like the last. Although it is a bit better defended, it should still be easy.