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Replying to the alien commander subject:

1)I have plenty of free space in alien containments (no research is avaible, i assume because there are no living aliens on the base) and after the status screen, it says that captured alien died because ther is no free room in alien containment

2) i am sure the commander didnt die, because i shot it with stun launcher, and inspected with my soldier (placing it to the backpack )

Maybe i'll transfer my avenger to anothr base (with built alien containment) and start affack from there.

Thx for the other answers!