Theory:Doctor Who television discontinuity and plot holes/The Doctor Falls


 * How were the rifles upgrades? And if every rifles was upgraded, so why wasn't Bill destroyed when she was shot at by accident?
 * The rifles weren't upgraded. It was just Nardole hacking the spaceship and exploding parts of it. The rifle shot was a deception, to fool Cybermen into believing humans have serious weapons.
 * Why didn't Nardole just blow up parts of the ship that contained Cybermen?
 * As he blew them up by igniting fuel pipes on the floor, due to it having been a solar farm. He'd need all the floors to be one, which they aren't.


 * Did something happen to the programming of the Cybermen, cause, I thought they only went after "humans" with 2 hearts!
 * The definition was expanded to include humanoids with two hearts. So they were still heading after normal humans too. Better question, could Nardole still have went down there safely and reprogrammed the computer to discount all humanoids from their protocol? They weren't targeting him before so unless he happens to have two hearts, it's unlikely the Doctor's upgrade would have included him too.
 * Your question needs separating.


 * How comes the Doctor can remember what Clara looks like all of a sudden? His mind was wiped of what she looked like in Hell Bent, but he has a vision of her before waking up.
 * Perhaps that was for our benefit and not what he actually saw? Also, he is dying, perhaps he briefly bypassed it. Note, he was in the TARDIS when it occurred.
 * It is also possible that he regained his full memories at some point. He has had a while to recover. (There are also theories out there that suggest the mind-wipe never worked at all, but I'm not suggesting that.)
 * He did see the waitress's face painted onto his TARDIS, and she diapered in a TARDIS so he could probably put 2+2 together to work out what she looked like. That or one or two memories slipped through the neural block, or the TARDIS does have telepathic circuits and archives or past companions. Or it might have been for the audience's benefit and the Doctor may have just imagined her.
 * The process of regeneration has begun and has repaired the damage done by the potion which inhibited his memories
 * Perhaps, it was simply a production error (Rory wasn't there)!


 * It is suggested that they could all escape in the Doctors TARDIS, but by the time they get to the top floor the Cybermen would have upgraded enough to stop them, so how do Heather and Bill get to the TARDIS without getting killed?
 * They are sentient oil, different physics. Plus, the Doctor killed practically all of them when he ignited floor 0507, so it's likely the condition of the Cybermen reset some hundred years.


 * Because of the above, couldn't Heather and Bill have saved Nardole and all the children?
 * Perhaps but they were living in peace and the Doctor implied it was something of a penance for Nardole for his crimes in life. Maybe they felt it fit to let him serve that. Secondly, maybe the Cybermen are defeated so they are free to live out their lives there forever. Also, maybe they did rescue them, we just didn't see it?


 * So did Bill revive the Doctor or was his regenerative process just taking it's time starting? Cause if the latter, shouldn't he be dead, as regeneration has proved that once it starts it has to finish or they die (it started either earlier when he fell against that tree or when the energy came out of his hand after being blasted). Also, shouldn't him resisting the regeneration have caused his death? The Master died when he resisted the process in Last of the Time Lords
 * He had been regenerating all episode, possibly prior to that. His body was already injured to trigger the process so moments like when he leant against the tree, when he was kneeling in the forest. Maybe it was just enough to keep his strength up and keep him alive, but he keeps resisting the full regeneration. The 8th Doctor didn't regenerate for a while after dying, the process was just taking longer. However Bill had hope so maybe that had an affect.
 * So is it delayed regeneration of Bill's tears? You're last line leaves it inconclusive.


 * Did I miss something, did we actually find out what crime Missy had committed to be imprisoned for a thousands years in a vault?
 * It wasn't revealed, but it's hardly a continuity problem, similar to how River Song's unknown crime didn't hurt the narrative.