So it was really bugging me that I only encountered Sectoid Commanders a couple of times (literally 2 missions, the base assault and a mission shortly after that), because I didn't manage to interrogate one, and then they just stopped showing up. However, just now, I've had an epiphany as to why that is: depending on what stage of the story you've advanced to, there are particular enemies that are designated as UFO captains. In the early game, it's the Outsider guys made out of crystal. If you shoot down a UFO or find one that has landed, you're likely to encounter those guys. Eventually, you encounter a Sectoid Commander during the base assault, at which point you'll stop seeing Outsiders for the rest of the game, as far as I can tell. And then eventually you'll encounter an Ethereal, at which point Sectoid Commanders are phased out, and Ethereals are the only enemy types you'll find as the leader of a UFO.
I don't know. I took down a fairly large ship that had sectoid commanders as the frist enemies I encountered and an ethereal as the ship's "captain." I'm still seeing every enemy type except for basic sectoids and I think I'm nearing the end of the game.
Saw an Outsider maybe twice. Once when I first met it and the second time when I captured it, then never again, so I think your theory is pretty plausible. Although I did continue seeing Sectoid Commanders well into the late stages of the game.
I don't know. I took down a fairly large ship that had sectoid commanders as the frist enemies I encountered and an ethereal as the ship's "captain." I'm still seeing every enemy type except for basic sectoids and I think I'm nearing the end of the game.
Now that you mention it, the one non-base time I encountered Sectoid Commanders, I encountered 2 of them in like the first room of a large UFO, which does kind of hurt my theory, as does your account.
Full disclosure: I have a save right before the final mission. I reloaded it a bunch of times recently, repeatedly scanning for activity, shooting down UFOs, and seeing what kind of enemy types I get. I still very rarely get Sectoids and Floaters, though Thin Men continue to be surprisingly common. But I haven't seen an Outsider in like 15 hours, and at least on my playthrough, Sectoid Commanders have been ridiculously scarce. Seriously, I reloaded that save like a dozen times and shot down all different sizes of UFO, and none of them contained Sectoid Commanders, but there was an Ethereal listed on like 80% of them.
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