Mission One - Surprise

At the beginning of the mission, you'll be under the command of Major Jackass.  Your objective is easy, just sit back and relax at the base.  When Major Jackass and Lt. Spock reach the base, they will be attacked and destroyed(?).  The Base will then come under you command.  Build a strong defense (Gun Towers and Chain Gun Turrets) to the West side of your base.  Build Extra power and have service trucks ready.  About 5 minutes after Major Jackass is destroyed(?), a squad of Assimilated Sabre Tanks will attack.  The Tanks are equip with absorption shields and heavy armor, so energy weapons are not that effective.  The Tanks also have a High Powered Borg Plasma Torpedoes.  These babies do heavy damage!  They can take out a scout in 2 shots, and have a med reload time.  After the first assault, expect more 4 squad assaults until the end of the mission.  Start building squads of tanks and scouts or your favorite hover tank that you use to follow and protect you.  When General Williams tells you to go to the base, take your squad with you.  You'll be surprised by 3 alien cubes.  They have heavy armor and high regeneration capability.  Once you take out the cubes, build an assault force to take out the enemy's base of operations which is located in the mid North West.  They are fortified with Assimilated Gun Towers and 8 cubes.  I suggest using the Bomber to take out the Gun Towers.  The Towers regenerate their health at a fast rate.  What takes 5 tanks to give 75% damage only takes them 3 minutes to regain!
 

Mission Two - Allies

You start off on the upper right hand corner of the map.  There is a scion base on the bottom of the map.  The Scions have a major disadvantage against the BORG, almost all of the Scion Weapons are energy based, which is repelled by the Absorption Shields the Borg have.  Start building a defense immediately!  About 5 to 10 minutes in the game, you will get a call from the Scion Commander asking for assistance.  Here you need to protect the scion's Recycler as well as yours.  A good ideal is to send a constructor down there at the start of the mission.   Set up a Relay Bunker there and Gun Towers there.  Than return to your base and use the Sat. Mode to work at their base.  About 20 minutes later after the distress call from the Scion Commander, you are given permission to attack the Borg.  The Scions will assist you, so take advantage of this.  A good Ideal would be to use Assault tanks against the gun towers to lower there defense to allow the scions units to get through.  The Borg Recycler is heavily guarded, so try bombing the Recycler before your final assault, this will weaken all units around the Recycler.