Good summing up of the plot so far. I think that covers the general direction of what we had in mind. 

I think if we did a little prologue scene for each of our characters, of their day-to-day life, before the circumstances that lead to their 'disappearing' that would be a good way to start?

As for the aliens, what do you think they should be like? Otherworldly energy beings, or more physical creatures? Individuals or more insect-like with a shared mind, or even elements of both?
I'm fine with any of those, but I'd suggest having them as 'physical' creatures would make it more interesting and easier to interact with them. Perhaps they could be somewhat insect-like, and very adaptable, using the genetics and technology of other species to improve themselves, so there's a wide array of 'sub-species' within their number. They could have a hive-like social structure, but still be individuals in character/personality, but vary in intelligence depending on their 'caste' and the needs of their 'place' in their society?! 
I'm just throwing out ideas xD

Should we put up CS's as well? I think that might be a good plan.