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In the Doctor Who episode "Before the Flood" (episode 4 series 9), the Doctor climbs into the stasis chamber in order to avoid the dam flood. Does this mean he remained in the chamber for years before arriving in the underwater station?

Also, how could he both be in the stasis chamber at the end of the episode and not at the beginning of the episode?

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Yes, he was in the stasis chamber all the way through.

Which means for 139 years: from 1980 to 2119. But because it was a stasis chamber, he didn't age during that time, and it must have felt like only a moment for him. He'd programmed the chamber to open at the right moment on the instructions of his own 'ghost':

CLARA: And [your ghost] saying the chamber will open?
DOCTOR: That was me telling me to get inside and when to set it for.

morning breath

As for your second question, he entered the stasis chamber off-stage while we were watching the Fisher King, shortly before the dam burst. Throughout the episode Under the Lake, he was both out in the base (where we saw him then) and also in the stasis chamber. But such is the nature of time travel: people can be in two places at once, as we also saw earlier on in Before the Flood when two copies of the Doctor and Bennett almost encountered each other.

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    @tilley31: well, these episodes were credited to Toby Whithouse, and at least he put an explanation of the bootstrap paradox in the episode. Moffat did no such thing in The Big Bang. – Paul D. Waite Oct 12 '15 at 23:18
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    @PaulD.Waite No, we always have to blame Moffat. He's like the Richard of Doctor Who. – Rand al'Thor Oct 12 '15 at 23:19
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    The thing that really got me with this two parter, funnily enough, is the length they went to to explain the paradox. That paradox has been employed numerous times on Doctor Who before but waved away. Now suddenly it's treated as a big deal; that felt a bit odd. – Lightness Races with Monica Oct 12 '15 at 23:21
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    However... "Google it" lol – Lightness Races with Monica Oct 12 '15 at 23:21
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    The Doctor programmed it to open. He tells Clara that when he is pointing out the bootstrap paradox to her. He says something like "The words I were saying were messages to me. Your name in the order made me face the Fisher King when I did and they told me when to set the stasis chamber for." – Etan Reisner Oct 13 '15 at 2:32

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