Well if that's the case then what if we throw in a wild card? This isn't the first mission so obviously we would think this routine however we have something unexpected happen. For example it could really be a trap where the enemy instead expected us to come and wanted to test a new nightmare frame. 

If you want to be more subtle you could have the commander be related to someone of high birth from Britannia thus in the long run giving someone an ax to grind against us. From what I remembered code Geass was all about betrayal and revenge from one person's point of view or another's. 

If that doesn't work we could go a bit extreme and say that along with the fact you destroyed the base you could have many of the workers be Japanese thus making it harder for you to gain the people in the future. 

How are those?