First Area
In the beginning, you will see an intro with 3 dropships and a Medic talking. When they first unload, you will have 8 Marines, 4 Medics and 3 Pilots. The easiest way to destroy the bunkers here is to have the enemy shoot your Medics first. Hold position your Medics and keep them close, so that they can heal each other. While your enemies shoot your Medics, just have your Marines shoot at the bunker. The enemies will keep shooting at your Medics until the bunker is destroyed. Follow through for the rest of the stage. If you do not want to destroy the bunkers, just run the pilots to each beacon while your Medics are under attack; as mentioned before, the enemy will keep shooting the Medics.
Second Area
You are provided with 3 Medics, 3 Ghosts and 4 Pilots. There are 3 siege tanks on the higher platforms. You may choose to blind the siege tanks with the Medics, cast Lockdown with the Ghosts and/or attack them. Blinding is easiest to do, since it will permanently keep the tanks for seeing your units. Lockdown, however, is not permanent and will cost you more energy. Keep in mind, it is not ideal to attack the siege tanks, since you cannot see them unless they repeatedly fire at you. Once the tanks are settled, just let the pilots run to the beacons themselves.
Third Area
You are given 4 Ghosts, 5 Medics, 5 Pilots, 2 Marines and 2 Goliaths. You have four opportunities to nuke. Although it's recommended that you nuke everything, it's up to you whether to use all your nukes or not.
The first enemy group has a Science Vessel in front. You must either use Lockdown or Optical Flare to prevent it from detecting your ghosts. Once it is done, launch a nuke in the middle (preferably on the first enemy Vulture you see).
The second and third enemy groups have Bunkers, Siege Tanks and Missile Turrets. You can nuke them on the high platform once you climb up. To take out the enemies inside the bunkers (preferably the second group), you can use your other forces, or just the cloaked ghosts. If you want, you can launch your fourth nuke again on the third group to take out the infantry from those bunker (and the spider mine, if you haven't destroyed it already).
Fourth Area
You are given 2 Marines, 2 Goliaths, 4 Ghosts, 2 Siege Tanks, 6 Medics and 6 Pilots. The first thing you should do is to select a Medic and use restoration on your siege tanks when the enemy ghosts lock them down. Once the ghosts are killed, siege your tanks (an enemy Goliath should be on his way, so break him down once you see him).
There are many different things you can do here. The easiest thing to do is to lockdown the first enemy siege tank, and have all your infantry and goliaths attack it. Then you should cloak your ghosts, lockdown the adjacent Science Vessel and destroy it. Whenever possible, use your two siege tanks to destroy the enemy defense. To do this, you must lockdown the enemy siege tank first. Follow through for the rest of the map, and all your men will survive.
The Main Shipyard
If you managed to steal all the battlecruisers, you should have 18 of them. Now you have no choice but to win, unless you fool around on purpose. General Duke will only bring 12 battlecruisers when the timer ends. You have all the upgrades (and the Yamato Gun!) but they have nothing. If you want to save as many battlecruisers as possible or to end the game quickly, group your battlecruisers into 9 groups of twos. Select each group to perform Yamato Gun on an enemy target. 2 Yamato Guns will not kill a full HP battlecruiser, but will weaken them enough for your other battlecruisers to destroy them really quickly.