With mixed reviews from critics and viewers I decided to give my opinions on the latest season of doctor who and how everything fits into the existing timeline as set out in the previous seasons, how his regeneration works and why the doctor behaves as he presently does.
Following on from the silence timeline the current regeneration is essentially a blank slate with clara having erased all knowledge of the doctor from history which leads to the inevitable confrontation at river song’s birth in which the doctor is known to be the enemy of the universe and a soldier, the previous season attempted to throw people off with the implimentation of john hurt as a soldier incarnation, however this was already a past regeneration and not the one in question on the timeline, also the whole plot of losing gallifrey is a little silly because they know it exists in the pocket dimension inside the painting itself, and even visited it during that episode.
All of this aside there were some other potential flaws in the writing in where matt smith had began a regeneration cycle on the beach where the silence’s plan to eliminate him culminates in a fixed point where river succeeds, however because of her love for him she decides to give up all of her regenerations to save him, this could have been done in such a manner that already overwrote the 13 lives issue, having provided all of her regeneration energy. Instead though they decided that as she was “dying” in the future anyway that it didn’t matter, but also to provide an alternative method of providing further life to the doctor with the timelord race itself providing energy through a crack on trensalore to help him to regenerate anew.
Hints towards the conclusion at river’s birth were given in this final episode of the last season where he meets the young soldiers that inevitably meet him there, and how the silence from that day vow to eliminate the doctor, which is a timeline that has already passed, as such wibby wobbly nature of time and plots.
Furthermore there are many unexplored themes in the series such as river marrying the doctor who clicks his fingers and the tardis responds as second nature, not just experimentation as previous doctors have done. Also a future doctor still has to provide river with his sonic and associated memory storing device in order to save her to the computer, so this is yet to happen in the series thus showing the doctor always lived beyond trensalore.
In order to correct potential paradoxes you will notice that clara is travelling to her existences through spacetime, she has interfaced with the brain of the dalek in the episode where they travel inside, inevitably she will end up back in the victorian era yet again, perhaps at a point where she loses her mind and ends up abandonned in the past, or at least pretends not to know the doctor so as to maintain continuity.
Lastly you will note that “missy” keeps appearing in a garden of eden place much like that of the computer in which river is stored in the library of the Vashta Nerada, and although these individuals have died they can still be saved in much the same way that river was saved, with hidden memory storage devices that can be collected later, and obviousely dropped off in time discreetly without the doctor noticing. To the individual involved they will die and awake inside the computer, and this can even pass to those who were killed by the brain sucking monster, thier body died but thier brain could have been saved and backed up prior to this.
So how does the doctor free these people, well given that the doctor and river are travelling at opposite ends of the spectrum, and she knew the first day he met her and didn’t recognise her she would die it would be a given that the same would happen where he would meet her and the first instance where he meets river and she doesn’t recognise him would be the day he knows he is going to die, and at this point being smart he would realise he has the opportunity to harness his regeneration energy and feed it into the computer to free river and the others, either by entering it himself entirely or just linking to it and running his energy through it and into the teleporter system to restore those who didn’t have bodies giving up some of his own regeneration energy.
At this point river should explain how he cannot regenerate in his current nature, as a soldier as he doesn’t stand for what the doctor stands for, and a healer of time while he stands for death and not caring about saving each and every individual whatever thier race and the idealism that comes naturally from the doctor, and provide him the opportunity to travel through time and save everyone he let down himself in the same way he saved her allowing the next regeneration to truly be a rebirth of the doctor.
Why missy though, well simply put the computer is able to rewrite the programming of people, within the computer river would be able to be restored as a timelord with all of her regenerations, and she could choose to regenerate anew inside the computer, and also when reborn out of the computer to also have a new start with the doctor both now travelling through time in the same direction together.
These are just my theories and idea’s, and fit the timeline and current events rather well wether or not this is how things progress will remain to be seen, but it makes sense that the current doctor would behave as he is doing given the timeline and established continuency of time from previous events.
It should also be noted that peter capaldi’s eyes appear in the day of the doctor episode when they state “13 doctors” during the transportation of gallifrey from the space time continuum into a painting, so obviousely he would have to return to that point to collect it, and obviousely he would be the safeguarder of the painting. This is also an inevitable spoiler that he already would survive beyond the battle of trensalore, which was already shown in other ways but this particular way is the biggest spoiler considering he has already regenerated beyond it at that point. Wether or not this has an influence on gallifrey offering up extra regenerations to him remains to be seen, but he could influence them considering without him being there to save them they wouldn’t survive in the pocket universe.