That was a fun afternoon. For those of you who don't know/struggle with the mission:
Focus all efforts on researching and building an Eagle APC. Fly it in manually and pick up the commander. This is the quickest way to complete the mission, for those of you who just want to get it over with.
You can beat the entire mission using only the commander; however it takes a long time, and requires proficiency in first person mode. I used the enemy vortex singularity machines to my advantage by standing near buildings I wanted destroyed and letting them do most of the work. The range on the commander's guns is what helps the most; you can take out all of the turrets if you inch towards them, your shots will still register as hits but the enemy turret won't start shooting back unless you get a little closer. The strategy I used was to bait all of the enemy machines back and walk backwards while firing at them. Was able to completely destroy the enemy base and walk out towards my waiting "rescue party" which had not moved at all during the mission.
The "fun" way is to fly in an Eagle APC and drop off a strike team of Templar Knights and have them destroy everything. I set them to high initiative and to attack buildings while I gave them cover. The high initiative made them smart enough to attack anything hostile that got too close.
Anyway, this and Take The Pass are one of my favorite missions, as well as the one before the last mission. If you have any difficulties with the campaign, let me know and I'll give you some advice!