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I assaulted the alien base and killed the sectoid commander. Shortly after that I shot down the overseer ship and made the game progress forwards. Now I never see any sectoid commanders and instead only fight ethereals. Unfortunately I never got to capture a sectoid commander alive.

Did I miss my chance to capture them? Do they stop spawning once I shift the stage of the invasion? Finally are there any other enemy types I could have missed?

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Could very well be. I haven't seen any Outsiders since assaulting the alien base. –  SaintWacko Oct 12 '12 at 17:25
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though technically outsiders aren't missable since you can't assault the alien base without having captured one earlier –  z ' Oct 12 '12 at 18:29
    
Perhaps I should redesign the question to "What enemies stop appearing if any stop appearing at what stages" or something. Don't know how to word it. –  Shykin Oct 12 '12 at 18:30

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If you've seen an alien once, you will see them again, this applies to all enemies except for the final boss and Outsiders (of whom you only need to capture 2). Grounded UFOs will occasionally contain Commanders and always Ethereals, the 2 enemies that seem kind of one-offish. The frequency of earlier enemies spawning does seem to go down as you progress through the game, but if you try for a while you'll meet them again.

Bonus: when you reach the final stage of the plot (but don't start it), you will be able to play pretty much forever, allowing you to complete all interrogations, research and foundry projects - no abductions to cause panic and no pressure to pursue the plot.

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Bad luck then that I never saw a sectoid commander again? I can believe that. But what about outsiders? –  Shykin Oct 13 '12 at 21:44
    
@Shykin I once had the pleasure of fighting 3 commanders at the same time, so the one at the base is definitely not the only one. They are quite rare though. Outsiders do indeed stop spawning, but then again you only need to capture 2. –  kotekzot Oct 13 '12 at 22:08
    
Makes sense they stop spawning once you've gained all you can from them. So the commanders you fought, were they after or before fighting your first ethreal? –  Shykin Oct 14 '12 at 3:26
    
I may have encountered them before the Ethereal, I haven't paid much attention. Interrogating one is necessary to finish the plot, so I doubt they stop spawning until you've completed the interrogation. –  kotekzot Oct 14 '12 at 5:45
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I can confirm that Sectoid Commanders do appear after the one in the alien base. I failed to capture that one too, but just yesterday, I encountered two of them in a random large UFO that had landed. –  pleinolijf Oct 18 '12 at 10:58

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