Happens Offscreen, but a CMOA nonetheless: In one of the earlier missions, you are sent to rescue a professor. After battling through several groups of enemies, you come across a man in a lab coat; it's his assistant. Dialogue ensues, then he runs off to the observatory to find the Doctor. Here's the thing: Exploring the room the assistant is found in will reveal a dead Sectoid, it's head crushed by a fire extinguisher.
Also, he manages not only to get through to the doctor far in advance of you, through several lines of alien defences, but also ends up making a Heroic Sacrifice despite having been an alien infiltrator the whole time.
Alternatively, that fact completely explains - and utterly negates - the CMOA - it's very, very easy to make good time through "hostile" forces if said hostiles believe you to be a friendly, and the Outsiders in The Bureau don't have any compunctions about killing Sectoids, so Lawrence's smashing a Sectoid's brains in if it didn't recognize him as a friendly (or correctly deduced that he had turned coat and needed to be eliminated,) or just to maintain his cover with Dr. Weir, wouldn't be amiss at all. (And it's not like greys are particularly hard to kill with fisticuffs, let alone a robust fire extinguisher as a melee weapon.)
Generally speaking, whoever thought up the Plot Twist that comes at the tail end of the game. While most of the game is So Okay, It's Average, the fact that you are playing as a benevolent Ethereal instead of William Carter makes everything that much cooler.