I’ve attempted to make sense of the plot of Series 5-7 of Doctor Who (up to and including The Time of the Doctor). I’ll have to heavily summarise this in order to put it in infographic form, but here’s the full version of my write-up in case anyone’s interested. I’ve pointed out all the timeline changes as long as they pertain to the series arc (unlike the re-writing of Kazran Sardick ), the plot holes, and my attempts to paper over some of them.
I warn you, it’s pretty long. Here we go:
* Amy’s parents erased by Crack, she lives with her Aunt.
* The Doctor crashes TARDIS in her back garden, seals the Crack, but not before Prisoner Zero escapes.
* Amelia waits all night out in the garden for the Doctor, and wouldn’t meet him again until twelve years later, but she dreams of the TARDIS coming back for her in the morning as a child (bleed from T7).
* Her Aunt sends her to psychiatrists because of her insistence in the Doctor’s existence.
* Madam Kovarian’s sect of the Papal Mainframe have a plot to blow up the TARDIS before the Doctor can get to the fields of Trenzalore. Other species know that the TARDIS will explode and think it will be the Doctor’s doing, so they plan to shut him in the Pandorica before he does so.
* The Cracks have also eaten the ducks of the duck pond, the Cyberking and the Daleks that invaded Earth.
* Amy and Rory see future versions of themselves wave back at them in Wales in 2020.
Headscratcher: How does Amy exist if her parents got eaten by the Crack?
Possible answer: What gets eaten by the Crack ceases to exist from that point onwards and it’s people’s memories of their existence up to that point that get erased. Physical imprints of their existence remain, including children. Could also apply to T2 for the photograph left behind of Rory and the existence of River Song, and for T5 for all the events where the Doctor saved the world and, again, the existence of River Song.
T1->T2 Rory gets eaten by crack
* Same as T1 but Rory doesn’t exist. Only future Amy exists to wave back at her past self in Wales in 2020.
* However, echoes of him remain: photographs and memories at the back of Amy’s mind that are enough for Rory’s consciousness to fully re-awaken in the body of a plastic Auton created by the Anti-Doctor League that trap the Doctor in the Pandorica.
Headscratcher: How does River Song exist if Rory is a plastic Auton and ceased to exist in human form before River was conceived? (see answer in T1)
Headscratcher: If the Doctor is known to be present at the fields of Trenzalore, why is River Song imprisoned for supposedly killing him earlier in his timeline?
Headscratcher: If the plot to have the Doctor killed at Lake Silencio is in place, why explode the TARDIS and the Universe before that happens in the Doctor’s timeline?
Possible answer: Stopping the Doctor from reaching Trenzalore by exploding the TARDIS was Plan A, Lake Silencio was Plan B. Or, maybe without the events of The Big Bang Amy might have changed her mind about marrying Rory, so River Song, whom they need for Lake Silencio, wouldn’t have been conceived.
Speculation: Only the Silence know about the Fields of Trenzalore and the phrase “Silence will Fall” is misinterpreted by other races as referring to the destruction of the Universe by the TARDIS exploding. It’s only after the reboot of the Universe that the association of the phrase ‘Silence will Fall’ with Trenzalore and the asking of the question become known.
T2->T3 TARDIS explodes. Universe begins to collapse
* No more stars. Earth is the last living place in the cosmos, with the exploding TARDIS acting as its Sun.
* Amelia remembers stars (the crack in her bedroom is still responsible for the absence of her parents and the echoes of things lost)
* The Doctor doesn’t crash in her garden but she meets him, Amy and Rory that survive from T2 in the Museum.
* The collapse of the Universe has affected parts of Earth’s history, as seen in the Museum exhibits. Soon, even the inhabitants of Earth begin to wink out like the stars did, this happens to the Amelia from this timeline.
T3->T2->T1 The Doctor pilots the Pandorica into the exploding TARDIS inducing a reboot of the Universe. As the Doctor travels back through his timeline, Amy can sometimes hear him.
T1->T4 The Doctor finds Amelia in the garden and takes her back inside and tells her the story of an old, new, borrowed blue box as she sleeps.
T4->T5 The Doctor walks into the Crack which seals behind him, and he’s deleted from the Universe except from Amy’s memories. The reboot of the Universe is then complete.
* Amy’s parents exist (as do the ducks in the duck pond!), while the Doctor never did, and with no Crack Prisoner Zero never invaded Amy’s home.
Speculation: Amy’s memories of the timeline where her parents had been eaten by the Crack and the Doctor crashed in her garden persist. She wakes up surprised to see her parents, because in her dreams she had been parent-less.
* Throughout her childhood she tells stories of the Doctor, and her parents send her to psychiatrists.
Headscratcher: Without the existence of the Doctor and the TARDIS, how does River Song exist? And why hasn’t the Universe gone to Hell like in Turn Left? (see answer in T1)
T5->T6 Amy remembers her travels with the Doctor
* Once Amy remembers the Doctor thanks to the trigger from T4, not merely her meeting with him as a child, but the time she travelled with him in the TARDIS, he’s brought back into the Universe, along with everyone’s memories of the events he was involved in as far as the writers want to reference in future episodes.
* Rory, having been a time traveller, also remembers events from deleted timelines, such as Prisoner Zero terrorizing Leadworth (T1) and spending 2000 years as a plastic Roman (T3).
* Until The Wedding of River Song, the entirety of Series 6 takes place in T6. There’s a lot of time travel here, but it’s closed loops within one timeline.
* Amy gets pregnant on her wedding night in the TARDIS.
* Amy witnesses the future Doctor’s death at Lake Silencio in 2012 at the hands of someone in a space suit in The Impossible Astronaut.
* They travel to 1969, where Amy is kidnapped by the Silence in ‘The Day of the Moon’ and replaced with a Ganger. Her real self is taken to Demon’s Run, where she unconsciously remotely controls her Ganger self that’s travelling with Rory and the Doctor.
* The Doctor uncovers the Ganger just as Amy is about to give birth in Demon’s Run. He and Rory go to Demon’s Run to get her and baby Melody who, having been conceived on the TARDIS, is a sort of Time Lord. They fail to rescue Melody, but find out she grows up to be River Song (the origin of the name being the translation of Melody Pond into the language of the Forest, where there is no word for ‘pond’ as all the water in the Forest is in the river, in Lorna Bucket’s prayer leaf).
* Melody is taken by Madame Kovarian’s people to 1960s America where she’s trapped in a space suit and conditioned to kill the Doctor (and the Silence settle on Earth long before that in order to manipulate humans to achieve the level of technology needed in order to invent said space suit by then).
* Little Melody manages to break free of the space suit in 1969 (messing up Madame Kovarian’s plan to bring Melody up to kill the Doctor freely in 2011) and manages to reach Leadworth, England by beginning of the 90s in order to grow up alongside Amy and Rory as their friend Mels.
* Amy and Rory have waited for the Doctor to return to them in Leadworth after the events of ‘A Good Man Goes to War’ and make a crop circle to call him to Earth. Mels barges her way into the TARDIS with them, and they crashland in Nazi Germany.
* Mels gets shot and regenerates into the form familiar as River Song. She poisons the Doctor. She learns about the name she will use and the future she will have with the Doctor and is able to understand the TARDIS, and trusting the word of her parents that the Doctor is worth saving, gives up all her regenerations in order to save his life.
* River is weakened after her sacrifice, so the Doctor takes her to a hospital in the 51st century. He leaves her a brand new copy of the TARDIS diary she will use in her life as River Song. She decides to study archeology.
* The Doctor leaves Amy and Rory with a new home and car in Upper Leadworth in The God Complex.
* Madame Kovarian and co. find River in the 51st century and drag her back to Lake Silencio in 2011 in a space suit that controls her to ensure she kills the Doctor.
Headscratcher: Why bother to influence Earth history to invent a spacesuit rather than bring their own and why does the Doctor’s assassin need to be a Time Lord?
Possible answer: The agent being a Time Lord and the technology employed belonging to the time period rather than a future one help to make it a fixed point in time.
* The Doctor calls Amy (pre-Demon’s Run), Rory and River to Lake Silencio in 2011 to witness his death (and Canton to see his body), although in truth it’s actually a robot replica inside of which he’s hidden, which can also fake the appearance of regenerating.
T6->T6B River in the space suit manages to stop herself shooting the Doctor
* The unravelling of a fixed point in time causes all of history to converge in that single moment.
* Amy is leader of the group fighting against the Silence. She remembers the other timeline save for some things like Rory’s face! Here Rory works for her.
* Amy remembers Rory and lets Madame Kovarian die for what she did to Melody.
* When The Doctor and River touch each other they are transported back to that moment in Lake Silencio in T6. The Doctor, still inside a robot replica, marries River Song and shows her how she wouldn’t be killing him if she pulls the trigger.
T6B->T6 River in the space suit shoots the Doctor, fullfilling the fixed point in time, time continues as normal
* The River that witnesses it all, unlike pre-Demon’s Run Amy and Rory, knows that the Doctor isn’t really dead, but just pretends otherwise.
* The River in the space suit is sent to Stormcage prison for killing the Doctor.
Headscratcher: The Doctor allows River to be imprisoned for something she didn’t do, and for which she would have been unjustly charged anyway since it was the space suit that made her do it and there were no witnesses except her parents and her future self. He breaks her out of prison all the time, he could have broke her out permanently rather than keep dropping her back in again now that he knows the truth. Perhaps it’s River’s choice to remain in prison because she’d do anything that might help keep the Doctor safe, but it’d be nice for that to be explicit, since it’s a huge deal!
Headscratcher: How long did River spend in prison anyway? Lots of time, based on the amount of filled pages in her diary we see in ‘The Impossible Astronaut’, where she’s still imprisoned, and during which practically the entirety of their relationship happened if it’s true that they are meeting each other in reverse order and therefore that kiss in The Day of the Moon is one of the last from River’s point of view. I imagine this is not really the case, and that the Doctor (post-Lake Silencio) and River do meet each other a lot between the time she’s let out of prison and the Library, probably between The Angels Take Manhattan and The Snowmen from the Doctor’s point of view.
* On one of the occasions she breaks out of prison, she reveals to Amy and Rory (post-The God Complex, and who remember experiencing T6B) that the Doctor is still alive after all.
* BTW, Madame Kovarian should be alive in this timeline, and it’s not revealed what came of her.
* Still in T6, but the Doctor has used Silence technology to make sure all records of himself in the Universe are deleted (revealed in minisode in S7 boxset).
* Since there are now no records of River Song having killed anyone, she is freed from prison and becomes a Professor of Archeology.
* Meanwhile the Doctor has hooked back up with Amy and Rory. In the episode The Angels Take Manhattan, he takes them to present-day New York…
T6->T6C Weeping Angels take over Manhattan
* Weeping Angels have infested New York throughout it’s history, causing time distortions that make it difficult for the TARDIS to land there.
* A Weeping Angel in present-day New York sends Rory to the 1930s where he meets Professor River Song, who’s arrived there by vortex manipulator, which she uses as a homing beacon so that the Doctor and Amy can use the TARDIS to reach them.
* They encounter a Rory dying of old age, which suggests that a Weeping Angel in the 1930s will get him and send him even further back in time. The Weeping Angels have used the energy obtained from repeatedly sending people back in time to completely control the city, to the point where even the Statue of Liberty is a Weeping Angel.
* Rory and Amy throw themselves off a building to create a paradox by Rory dying before he’s supposed to in the current timeline.
T6C->T6 The paradox causes the Weeping Angel timeline to evaporate
* Amy and Rory find themselves in present-day New York, alive, as well as the Doctor and River. But there’s still a lot of temporal scar tissue, so the TARDIS can never land there in the 1930s again.
* A remaining Weeping Angel sends Rory back to the 1930s. Amy allows herself to also be sent back by the Weeping Angel to be reunited with him. The couple are destined to live out their lives there, as their graves in present-day New York can attest. The Doctor can never visit them or interfere with that destiny because that would risk seriously damaging the fabric of spacetime because of that scar tissue (explanation taken from Steven Moffat in DWM).
* River can nevertheless use her vortex manipulator to visit them in the past, and hand over to Amy a copy of a book called ‘The Angel’s Kiss’ by Melody Malone, which contains all the events that took place in the episode and which had essentially guided them throughout it. Amy is to copy out that book (ontological paradox) and publish it.
* ‘The Angel’s Kiss’ contains an Epilogue which is a message from Amy to the Doctor. In the present day, the Doctor, who had torn that page out earlier without looking at it, recovers it and reads it. In her message Amy asks him to find Amelia waiting in the garden and tell her about the wonderful adventures they’d have if they ever met again. It is unclear whether this is something Amy has already experienced in T6, or whether she’s asking him to make a change to the current timeline. Just in case she is…
T6->T7 The Doctor travels to when Amelia waited all night in the garden and gives her hope that they’ll meet again and have all sorts of adventures.
* Amelia carries the knowledge that she’ll meet the Doctor again with her until she does.
* A glimpse of this timeline bleeds into Amy’s dreams in T1.
Possible answer: A different version of the events at the beginning of The Eleventh Hour took place in T6, where there is no Crack but the Doctor still crashed into Amelia’s shed. Or, Amelia’s memories of other timelines prompted her to wait for the Doctor in the garden one night whether the Doctor crashed into her shed or not, and the Doctor meets her then.
* Having encountered two versions of the same person, Oswin Oswald in the Dalek Asylum and Clara Oswin Oswald in Victorian England, both of whom died, the Doctor searches for and ends up finding Clara Oswald in present-day London.
* River died in the Library. Her body was buried in Trenzalore but her consciousness was digitised and kept in the Library’s hardrive, from which she can escape.
* The Great Intelligence gets pissed off at the Doctor and lures him to Trenzalore. This is the Doctor’s future final resting place, and the dying TARDIS is his tomb. It holds his whole timeline. His real name is the password to open it. River’s consciousness follows Clara into Trenzalore and with the G.I. about to kill Clara and the Paternoster Gang, she utters the Doctor’s name to open the TARDIS.
Headscratcher: According to Silence in the Library, there is only one reason the Doctor would tell anyone his name, and only one time he could. Yet Clara is able to read it in a book in the TARDIS and according to River she got him to reveal it to her by nagging him till he did. Okay.
T7->T7B The GI enters the Doctor’s timeline, scatters into many versions of himself that undo all of the Doctor’s victories and make it like he never existed
* Without the Doctor’s influence in their lives, the Paternoster Gang wouldn’t be friends, so Strax turns on Vastra and Jenny disappears.
* The stars go out as all the corners of the Universe the Doctor saved are destroyed
T7B->T7 Clara enters the Doctor’s timeline after the GI, scatters into many versions of herself to save the Doctor’s life and reverse the damage done by the GI
* Mostly the many Claras that have appeared throughout his life go unnoticed by the Doctor, Oswin and Clara Oswald were the exceptions.
* The original GI got destroyed when entering the Doctor’s timeline and the same should have happened to the original Clara, but the Doctor saves her.
The Day of the Doctor
* Eleven and Ten are let into the Time War by the Moment just when the War Doctor was about to use it to destroy all of Gallifrey and the entire Dalek fleet that has surrounded the planet. They realise that instead they can freeze Gallifrey in time and transport it to a pocket Universe at the moment as the Daleks are about to fire, so the Daleks destroy themselves in the crossfire, while it appears that they got destroyed along with Gallifrey.
* Pulling off such a feat would require
Speculation: They, too, are allowed passage into the Time War by the Moment, and also forget these events, like Nine and Ten would.
Headscratcher: How does Nine have such realistic, intense, memories of destroying Gallifrey and the Daleks if supposedly he didn’t?
Possible answer: The Moment, able to access the Doctors thoughts, also gave him memories of an aborted timeline in which he did destroy Gallifrey and the Daleks.
Headscratcher: The depiction of the final day of the Time War as a Dalek invasion of a Gallifrey largely populated by children is completely inconsistent with previous descriptions of it. Quote from The End of Time Part 2: "Perhaps it’s time. This is only the furthest edge of the Time War. But at its heart, millions die every second, lost in bloodlust and insanity, with Time itself resurrecting them, to find new ways of dying over and over again. A travesty of life. Isn’t it better to end it at last?"
* Having done the deed, the Doctors go their separate ways. Gallifrey is somewhere in another Universe. Eleven meets someone who’s hinted to be a future version of himself who is retired and working as a curator at the National Gallery.
Headscratcher: Why isn’t the Doctor more surprised by the idea of meeting himself if he’s supposedly knows himself to be the last incarnation?
The Time of the Doctor
* The Doctor heads to Trenzalore, but before it’s the graveyard planet of ‘The Name of the Doctor’, and instead houses a town called Christmas. There’s one last remaining Crack. The Time Lords, in a different Universe, are using that Crack as a a tether and have let a truth field bleed through it to get the Doctor to speak his true name as a kind of password to confirm this is the right Universe so they can come through.
* Other species in the Universe want to destroy the planet rather than allow the possibility of it serving as a passage for the Time Lords. The Doctor knows that he can’t speak his name and allow the Time Lords passage while entire fleets await to go to war with them. So he decides to stay and defend Trenzalore from the invaders intent on destroying the planet, aided by the Papal Mainframa led by Tasha Lem. Because of War and 10.5, he’s already used up all his regenerations.
Headscratcher: If Eleven doesn’t have the capacity to regenerate, then why fake a regeneration lightshow at Lake Silencio? And more importantly, from where does he get the regeneration energy to heal River’s wrist in The Angels Take Manhattan?
Possible answer: Since he’s widely known as the Eleventh Doctor and the War Doctor is a secret, the regeneration lightshow made his death more convincing. And in TATM that was him giving years off his life to heal River (like Ten did in Rise of the Cybermen to recharge the TARDIS crystal) which he can only do thanks to the regeneration energy that River gave him in Let’s Kill Hitler in his system.
Headscratcher: But in Let’s Kill Hitler, when the Doctor is poisoned he tells hologram Amelia that maybe he should regenerate, but hologram Amelia tells him the poison has interrupted that ability. So there the Doctor thought he still had the capacity to regenerate and the TARDIS confirms that the capacity existed for it to be interrupted. Ehem.
* The Doctor fights for centuries and ages until his body can’t take it anymore.
Speculation: In other occasions the Doctor has lived centuries without aging, but warfare does age him, as happened with the War Doctor.
* Clara begs the Time Lords through the Crack to save the Doctor’s life.
Speculation: The Time Lords, aware of the stalemate, decide to give the Doctor more regenerations since he is their best chance of making it to this Universe, even if it means they have to seal the last Crack, since it won’t do them any good if he dies and Trenzalore is destroyed. They’re now banking on him finding another way.
T7->T8 The Doctor doesn’t die on Trenzalore, changing his future
* The Doctor uses his regeneration energy to defeat the invading Daleks and save the Christmas town before turning into Twelve.
Headscratcher: If the Doctor doesn’t die on Trenzalore, that means the events of ‘The Name of the Doctor’ can’t happen, Clara can’t become The Impossible Girl and so he would never have met her. Paradox! It would also mean the Great Intelligence is still out there.
Possible answer: Either:
a) The fact that the Doctor has already experienced a timeline in which he meets Clara, and since time travellers don’t forget aborted timelines, means that Clara and the Doctor will still know each other the same as ever after the timeline change
b) This paradox will be addressed as something that needs to be fixed in Series 8.
c) The Doctor will be buried at Trenzalore one day, just not just yet. Although it would make no sense for the TARDIS interior to be the current one. And rather depressing that Trenzalore becomes a graveyard planet anyway even though Christmas town was saved in the end.
Headscratcher: So Madame Kovarian’s plan to stop the Doctor from rescuing the Time Lords through the Crack on Trenzalore involves causing the explosion that creates the Cracks in the first place? Okay.
Any questions, feedback or suggestions are welcome, as well as any offers of help to put this in graphic form.