I find the Shogg arc to be have particularly interesting parallels for X-com's morale compass.
X-com finds a new world hitherto unknown to (our) civilisation.
It's populated by cultures that are clearly intelligent, they use tools and construct buildings, but we can't communicate with them, they are technologically inferior to us, and they look different to us. So we shoot them and nick their stuff.
Later as we get more information about the place we ally ourselves with a small local ruler whom we support and put into power, we then trade them guns in exchange for them attacking other Shogg factions on our behalf. (The scorpoid palace assault and acquiring the reptoid ship)
We now have a foot hold in this new land, not controlling it directly but though a local puppet leader, whom we 'help' but could easily destroy if they don't agree to cooperate with us.
This always strikes me as being extremely similar to how the British empire grew. And as I am British this means that X-com are clearly angels who can do no wrong