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Whenever the commander is in the battle room, her face is always covered by a white mask.

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I thought it might be some unexplained atmosphere thing, but when Yuhata is in the command center, she is perfectly fine without one.

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And it's not covering up a hideous wound, because we've seen her face before:

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Maybe this was explained before and I missed it, but why does she wear this during battle?

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    I think the anime has already explained/gave hint about it, but not in much details. She has undergone DNA treatment (or something similar) so that she can live beyond the age of a normal human. (I'm not 100% sure, but she got such treatment because she was one of the few who was left after the 4th Gauna War). Normal people are not supposed to see her face, because they would realize that she does not age at all during decades under her rule. – nhahtdh Jul 20 '14 at 16:22
  • Ah, that seems to ring a bell - I must have either forgotten or skipped over it when I was watching - you should post that as an answer – Toshinou Kyouko Jul 20 '14 at 16:30
  • I probably will post an answer tomorrow, since I need to get all the details straight. – nhahtdh Jul 20 '14 at 17:00
  • I was reading up on this and there are other characters who have lived equally as long, such as sidonia-no-kishi.wikia.com/wiki/Lala_Hiyama and sidonia-no-kishi.wikia.com/wiki/Yure_Shinatose, who don't seem to wear them. – Toshinou Kyouko Aug 16 '14 at 19:39
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It's been a while since this was asked and is pretty much covered in the comments, but here's an answer.

Captain Kobayashi is part of the immortal council and therefore doesn't age. If she walked around never aging people would notice, hence the mask. It probably also serves as a way to hide emotion from the crew, show strength and all that.

Sidonia's wikia page is pretty barren, but there is some stuff there.

  • Also allows her to walk around looking like a doctor, but not being known as the captain - it gives her the "disguise" of her own face. – EngrStudent Aug 21 '15 at 0:13
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I can't help but think that the mask is random and serve no particular purpose as with a lot of things in the show.

We see the Captain with the mask sometimes, and then we see her without in front of people, the mechanic team, some of the trainees. Same goes for Yunatose, at times she wears a mask then other times, even when she is at work, she does not.

As for the aging thing, I believe the Council takes turn to be Captain so they will change hand every couple of decades or so without the average people knowing about them. They will just assume that the Captain got old and replaced with a new guy. Also how come nobody mentions the teddy bear, how is she even around and nobody noticed she is immortal? So I guess it's just the mismatch of the writers.

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