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Space battles can get annoying sometimes if your not sure how to cripple you enemy. But if you think that tackling the enemy's capital ship is just to difficult than have I got a walk-through for you! Ok here goes.

First when you spawn, try to spawn in the hanger next to your troop transport. Make sure that you start as a pilot. So once your in the hanger and you have the troop transport, try to get as FEW other troops in the transport as possible.
Next thing ya do is fly the aforementioned transport to the enemy ship's hanger, don't worry about their anit-spacecraft turrets, the transports have additional shielding to make up for their crappy speed and manuverability.
Once your in the hanger, make sure that any additional passengers on the transport get out, if not they will take of and inebitably crash the transport into the wall. Crippling your troop count. If you cannot get all the troops out when you land take off and instantly land again, this will cause the other passengers to get off as well.
After you have all the troops out of the transport make a bee line for the enemy sheild generator (ignore any enemies you may see). The sheild generator is the far door from the enterance to the hangar. Once your in the sheild generator room walk streight up to the big glowing column in the center of the room and place a charge on it and step back. Once that charge detenates, repeat the process untill you have no charges left. You can get more from the gonk droid in the main room of the ship. When you have more charges finish off the sheild generator and you should hear a prompt telling you that the enemie shields are offline.
Re-enter the main room and place two charges on the center column to destroy it. This deactivates those pesky turrets on the exterior of the capital ship, making it easier for your allies to attack the external components. Get more charges and make you way into the two side rooms that contain the life support and engine cooling systems. Keep on your toes though, as both rooms are guarded by auto-turrets, which wont heistate to turn you into a cloud of red mist. You can dissable them for a while by standing directly under them (so they can't get you) and shoting them with you blaster till they explode. Finish off the remaining systems (life support and engine cooling) and head back to the hangar.
If you die while attempting all this, fear not. For you can respawn from the troop transport that you left in the enemy hangar.
Once you are back in the hanger swipe one of the enemy BOMBERS, and launch from the hanger. Attack the long-range sensors and the short range sensor array. Those are the last two components on the capital ship. The last big point bonus you can score is by destroying the enemie friget. These can be tough though as they cannot be boarded and destroyed internally. Just stay low so that their turrets can't get you and bombard them with bombs. While doing this use fansy airial manuvers to keep away from the enemy fighters, they will try to kill you once they figure out your harrassing their frigate.
If you destroy the frigate and do not instantly gain victory, shoot a few enemy fighters, bombers, and troop transports to gain those extra points.

So there ya have it, basically what the totorial tells ya, but in specific order with proper detail. If you need more help just ask, and I will do my best to be more specific. Have fun conquering the galaxy. May the force be with you!