The second GDI mission gives you more free will than the first. Charged with restoring the pentagon's defenses and eliminating the NOD presence, you will first want to attack-move your infantry into the pentagon's power plant area which is under attack. The NOD are so busy with their destruction, they'll ignore your riflemen killing their buddies. While the riflemen handle the militants, begin moving your engineers to capture the power plants. When three are captured, the pentagon's defenses will come to life and commence mowing down the NOD attackers. You'll need to send a fourth engineer into the pentagon itself to restore control. Finally, the nod will destroy the power plants, forcing you to send infantry into the guard towers to defend the area "the hard way". Use the attack-move to get your men into position, then put one in each tower.
When you have established defenses in the area, reinforcements will come in the form of 6 APCs. These are one of my personal favorite units in multiplayer, as they are extremely versatile in that they can be loaded with various infantry to perform specific roles. In this case, loading them with the grenadiers you acquire afterward seems prudent. Send the APCs with grenadiers to take out the NOD positions in the buildings to the northwest of the pentagon. Afterward, push your way to the north to eliminate the (marked by green) NOD outpost. I used all 8 APCs for this purpose to perform the task swiftly. The APCs with grenadiers inside will do great against the buildings and paltry infantry force protecting the area. Be sure to take out the barracks first, as it will pump out militant squads that will harass your APCs.
After the outpost is taken down, send your APCs to make their move on the NOD base proper. They will face some rocket bikes, which will not pose a great threat. I fought in the street between the buildings and the grenadiers' grenades really made an impact on the NOD presence there, hah. Again, you will likely want to eliminate the barracks first as the constant stream of reinforcements can be quite annoying. Once it's down, take down the Air Tower to halt the vertigo bombers' incessant pounding on the pentagon. Finally, tear up the other NOD structures to finish the mission.