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I have not seen this series for a while however I am reasonably confident the episode in question is "Allison from Palmdale", apologies if I am incorrect.

In one scene in the darkness of the future (or the world after the machines have taken over), the outside of what appears to be a docked large ship is shown. Either before or after that, we are shown a room inside the vessel containing cages of animals and if memory serves, humans as well.

The question is relatively simple: What was the purpose of Skynet collecting and keeping them? Was it likely for future study or is there more to this (either in- or out-of-universe)?

I could see why they might want human "specimens" for future study, but not immediately think why Skynet would also be interested in animals. Pretty sure the scene included both lions and monkeys, at least.

I did consider a "predator vs prey" study with animals by the machines but that in itself did not really seem fitting with any Skynet storyline.

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    Study, or repopulation, are the two most obvious answers.
    – Radhil
    Commented Jan 11, 2020 at 13:24
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    "Hunter-Killers: patrol machines built in automated factories. Most of us were rounded up, put in camps for orderly disposal. (pulls up his right sleeve, exposing a barcode) This is burned in by laser scan. Some of us were kept alive... to work... loading bodies. The disposal units ran night and day. We were that close to going out forever. But there was one man who taught us to fight, to storm the wire of the camps, to smash those metal motherfuckers into junk. He turned it around. He brought us back from the brink. His name is Connor. John Connor. Your son, Sarah, your unborn son."
    – Valorum
    Commented Jan 11, 2020 at 13:57
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    But why put them in camps for orderly disposal, why no just blow them up, or killem all. If Skynet was worried about waste, dead humans would be great fertilizer for plants. Commented Jan 11, 2020 at 17:15
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    @AlessandroSanfilippo - The same reason the Nazis switched from bullets to gas, because it's more efficient
    – Valorum
    Commented Jan 11, 2020 at 17:26
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    @Valorum It was more efficient for the Nazis because their officers kept getting traumatised by killing people and the gas was less psychologically damaging to them. That’s not an issue that the machines would have.
    – nick012000
    Commented Jan 11, 2020 at 20:56

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