Theory:Doctor Who television discontinuity and plot holes/Under the Lake


 * What did the crew do in the missing three days? Just run around like headless chickens getting supplies and finding somewhere to hide whilst dodging cutlery throwing ghosts? Not bother to contact the Main Base?
 * It presumably took them some time to realise that they were safe where they were, and that the ghosts didn't come out during the day. That, along with gathering supplies, investigating what was going on, occasional sleep, etc, probably accounts for the time.


 * I'm a little confused! The base is now underwater. I assume that the "city" was somehow flooded, and because it was flooded, there was no use for the "city" and everyone was evacuated. So why does the base have a computerised day and night setting?
 * The Base was probably build after the flooding.
 * A Day/Night system could easily be implemented.
 * The episode indicates in dialogue that the base was built after the oil deposits were discovered under the lake.


 * By this point we know the Doctor and Clara have been together for at least several years (due to the three-year time jump between when she was 24 in Bells of Saint John and 27 in Deep Breath, and then whatever time has elapsed since then). She's put herself into danger many times and the Doctor himself has put her into danger many times by this point. So why does he choose now to admonish her for putting herself into harm's way?
 * I think he sees that she's getting a little bit reckless with how she treats the adventures as exciting and action rather than something that can potentially kill her.
 * We also don't know precisely how long it's been since Danny's death and an ongoing plot thread for Series 9 is how after Danny's death she's grown more reckless.


 * O'Donnell all but ignores Clara when she's introduced and afterwards, yet she gushes over the Doctor declaring herself a fan and in the next episode name-drops a number of his recent companions, but again omits Clara. Given her fan-gushing one would think she'd be more friendly towards his companion, given she's aware of their significance.