That sounds like a good idea to me - breaking out in the middle of confusion would be good, as it'd give out characters some time to explore without being chased immediately, and a chance to get to know one another as well. And I agree about them being unconscious during the testing too, that makes sense. 

Creating the aliens could be fun too! I like the idea you suggested before, making them a bit like the Covenant from Halo, with a number of different races all working together.