So, i have been thinking an idea fr a new mod. How about this:
Early in the game after, after completing a few missions succesfuly, you start to receive mysterious transmission messages from some unknown place telling you about secret locations of alien landings. you can decide wether to accept or ignore the mission, but after succesfully completing three of this missions you will receive another transmission, this time requesting for your help because the invaders have located your mysterious informant's hiding spot nd are planning to kill him.
THe place is a small abandoned town (in the desert, maybe?) and as you advance you start to see sectoid corpses over the place.
you find and kill the enemy forces and your informant tells you were you will find him and the rest of the survivors, but warns you to not be afraid for what you see.
and then your troops find the mysterious informant is...A SECTOID COMMANDER!...oh, and four normal sectoids.
Ahem...now that that is done. the idea for the mod would be that there is a sectoid commander who had developed a mind of his own during his creation and tried to use his mental powers to do the same with his "brothers" but the ethereals discover him and he deserts to X-com.
you can then create aliens after taking down an alien ship and recovering a birth chamber like the ones the aliens use to increase their numbers(because i believe the aliens we face are artificially created instead of the natural process their ancestors probably had before the ethereals conquered them) and installing it in your base and you can then send them on missions while the sectoid commander stays behind.
And then it is all the usual gameplay with some comments from the sectoid commander about his insights in the aliens mentality. some musings about humanity and how different/similar they are from the ethereals and all that good stuff.