
Over the past day or so, however, I've been thinking how I could have made it work a little better, making it into a more cohesive and engaging series. These are just ideas, but most of them are considered as to how they would be put into practice, and with clear examples. I've also tried to stick to what was in the series (e.g.. things like Missy, Davros, Ashildir etc.), and not add in things that weren't there (like say Romana or Susan or Cybermen). This is an attempt to use the same resources to try and structure the season a little better, and to bring the plot arc into greater focus. I'll break it down episode by episode, explaining what changes I'd make and why I'd do it differently:
Episode 1: The Magician's Apprentice

Episode 2. The Witch's Familiar
Ok, so the Doctor is about to kill Davros, we get the reprise of the previous week, and then we see what happens next: Davros takes the gun off the Doctor, and points it at him, telling him to go to the Kaled city, to tell the Kaleds what the Doctor knows about the future. The audience now has an answer for the question posed in last week's instalment: no, the Doctor wouldn't be able to live with the knowledge that he'd killed young Davros, allowing him to falter, and for kid Davros to take control. The Doctor is returned to the city, and forced to reveal everything he knows about the future of the Kaleds and the Daleks. The Dalek programme is started earlier than it should be, with Davros leading it, even though he's only a child. The Doctor is left a prisoner of the Kaleds, as, thanks to his knowledge, the Daleks expand and conquer: first destroying the Mutos, then the Thals, and then spreading out to the rest of the universe. We then jump ahead a year: the Daleks are now spreading their empire far and wide, and the Web of Time is cracking apart because of the Doctor's actions. The Doctor is locked in a cell, where he is visited by Davros, who is basically now like a child version of Hitler. He taunts the Doctor, telling him if he'd left him to the Hand Mines, or had the guts to kill him, this would never have happened, and he could have saved so many billions of lives. At this point, we see the Doctor: not this all powerful legend, but the Doctor, as a man, completely broken. This is probably the lowest he could ever get. The conversation also includes talk about the Hybrid: this is the point where it's first mentioned, and Davros wonders whether it's the thing the Doctor fears the most. We also see the Confession Dial, and the Doctor tells Davros what it's for, setting up Heaven Sent. We cut away from this to Clara being summoned to UNIT: like in the original Magician's Apprentice, only with a context that's more justified. UNIT have detected a massive Dalek fleet approaching the Earth, and they need the help of the Doctor. Clara, however, hasn't seen the Doctor, and so UNIT put out a distress call, which is answered by Missy in her own TARDIS. She has detected that the universe is cracking apart, and the timelines are unravelling, and all of this is to do with the Doctor's knowledge having created the Dalek empire a thousand years too early. She takes Clara back to Skaro to rescue the Doctor, but makes it clear that she's only doing this to keep herself alive, and to stop all of reality collapsing (rather than the nebulous motives in the original). They manage to free him, and escape. The Doctor then takes Missy's TARDIS back in time, to the point when the Doctor shoots the Hand Mines to save young Davros. He considers killing Davros once and for all, something which Missy goads him towards, however Clara knows that killing Davros will just supplant one paradox for another. The Doctor decides to step outside Missy's TARDIS, and warn his earlier self not to take Davros back to the city, to just let him find his own way. The earlier Doctor agrees after seeing the agonised look on his future self's face and his ripped clothes, and leaves in the TARDIS. The future Doctor then leaves in Missy's TARDIS: he, Clara and Missy are the only three people in the universe who remember what happened, since they were outside of time when the time shift occurred. Reality catches up with itself, and Missy leaves the Doctor and Clara by the Doctor's TARDIS on Earth, where it has been displaced too. The Doctor and Clara then talk about the morality of the situation: in the end, they did just transplant one paradox for another, and the universe might still be feeling uncomfortable from that, setting up the end of the season.

Apart from a little bit of tightening, and removing the scene between the Doctor and Clara about a duty of care, there would be no major changes to this story.
Episode 4: Before The Flood
There would, again, be no major changes to this story. However, the end would hint towards the Doctor being more concerned about the possible damage to history caused by the Fisher King, and his own Bootstrap Paradox.
Episode 5: The Girl Who Died
Again, no major changes. However, the final scene would be different, with Clara being more uncertain about the Doctor's actions being right. Again, more mentions of the damage to the Web of Time and the Hybrid. Also, I'd get rid of the scene where Ashildir talks about how special she is, because that was just flat out stupid.
Episode 6: The Zygon Invasion
The only change to this story (apart from the Hybrid mention being removed) would be that it's now in a different place in the season (to allow The Woman Who Lived to feel a little more like it's own standalone thing).
Episode 7: The Zygon Inversion

Episode 8: Sleep No More
Moved for the same reason as Zygon Invasion & Inversion. Otherwise, no substantial changes.
Episode 9: The Woman Who Lived
The only major change with this script would be the placement, which would be done to allow a bit more breathing space between the two historical/Ashildir focused episodes. After all, many people (including DWM, surprisingly enough) felt that a gap between the two stories would have made the whole story arc flow a little bit better, and we may have been able to look at the Doctor's actions more objectively, and it would provide a nice lead into the final three episodes, looking at the Doctor's actions across the season.
Episode 10: Face The Raven
Ok, this is where the season shape really starts to change. So, most of the opening plays out as in the original: Rigsy has an odd tattoo, and the Doctor and Clara investigate a Trap Street, where they believe Rigsy got the tattoo. However, the only major difference in the first half hour is that, instead of meeting Ashildir on Trap Street, they instead find that the mayor is in fact Missy. The Doctor instantly doesn't trust what's going on, and senses that this is a trap, but knows he needs to help Rigsy. They basically carry out the murder-mystery part of the plot, and then they go to that house where the teleport device is: like in the original story. However, Missy finds them, and revels that she killed the woman whom Rigsy was framed for murdering: it was all part of a plan to bring the Doctor here. The Doctor realises that he has to try and save Rigsy's life, and orders Missy to release the lock. Missy threatens Rigsy's life: if the Doctor doesn't take the teleport as her masters demand, she'll let the raven kill Rigsy. The Doctor agrees, but Clara has already taken on the lock. The rest of the episode mostly remains the same, with Clara dying at the hands of the Raven, and the Doctor being angry with Missy before teleporting away.
Episode 11: Heaven Sent
Again, just like the original. This ones too good to tamper with, although it's now more tied more into the arc that has been created now.
Episode 12: Hell Bent
Right, this is huge. Most of the original story is cut: the barn, the banishing of Rassilon, the resurrection of Clara, the return of Ashildir etc.. The Doctor's back on Gallifrey, the Cloister Bell's are ringing, the Time Lords fear the end of the universe is coming. The Doctor goes STRAIGHT to the Capitol, saving all that pissing around with the barn, and talks to Rassilon and the High Council about the Hybrid. Missy is also on Gallifrey, and the Doctor realises that she was employed by the Time Lords to bring him to Gallifrey, which explains why she was on Earth in Dark Water: she was trying to bring the Doctor to Gallifrey. The Time Lords have detected that the Web of Time is collapsing, due to the Doctor's actions with Davros, the Fisher King and Ashildir, and they are worried that the Hybrid will emerge through the gaps in reality. The Doctor still believes that the Hybrid is himself, since he's caused all of these things, and tells the High Council. They decided to lock the Doctor in the Confession Dial, believing that the Doctor is the Hybrid. However, the General knows that the Doctor was manipulated into the situation by Davros and Missy. The General frees the Doctor, and they find that Missy is trying to access the energy of the Eye of Harmony. With history collapsing, Missy creates a rip in the time/space continuum, setting off a massive chain reaction: the Web needs to be sealed in order to heal, using a massive amount of energy for time to snap into place and absorb all the changes that have taken place. Missy, however, plans to hold the Time Lords to ransom: she'll use the singularity of the Eye of Harmony to close the Web and save all of time if the Time Lords make her President in Rassilon's place. That has been her plan ever since she was saved by the Doctor in Day Of The Doctor: to take control of Gallifrey. She was going to use the Doctor and her Cyberman army in Death In Heaven to overwhelm the Time Lords and take control, but when Danny Pink destroyed them, she changed her plan. By manipulating the Doctor's TARDIS, she brought him into contact with young Davros, putting the whole future of the universe in jeopardy. She knew that the timeline would be damaged, and the Doctor's other exploits (saving Ashildir and cheating death at the hands of the Fisher King) have weakened the structure of reality. Finally, the interference with the Eye has collapsed the walls of reality, and now Missy is destroying not just Gallifrey, but the whole fabric of time too. The Doctor tries to convince her to see sense, however before he can stop her, Rassilon arrives, determined to take control of the Web of Time himself. He knows that the Daleks weren't all defeated in the Time War, and they will inevitably threaten Gallifrey at some point again: he intends to wipe them from the timelines before they can. He has planned this since Gallifrey was frozen in time, and manipulated Missy in order to get the Doctor to change history: since Rassilon couldn't directly interfere, he elected to release Missy to find the Doctor, and bring history to it's knees in order for him to access the Web of Time. Missy and Rassilon try to step through the rip, but find themselves fighting to get in through the gateway. The Doctor pushes them through the fissure, and uses the great power of the Eye to close the fissure. Reality snaps into place, and time resets, with all the paradoxes fixed in place. Reality is no longer collapsing, and history is safe. Gallifrey is also free, from both Rassilon's tyrannical rule and Missy's insane vengeance. The Doctor still believes that he caused this, and was the Hybrid. However, the General tells him that the Doctor, nor Rassilon or Missy ever knew the full part of the prophecy: the Hybrid would have saved Gallifrey, not destroyed it. Like all legends, the tale got garbled and embellished in the telling. The Doctor was the Hybrid, but the Hybrid was destined to save Gallifrey. The General takes charge of Gallifrey, and recalls the Doctor's TARDIS, so he can continue his wandering. Before he leaves, however, he informs the Doctor that in the redraft of history that occurred when time snapped into place, Clara's death was averted. However, she never remembers travelling with him, and her life went down a different route. The Doctor leaves Gallifrey, going to see her. He finds her working at a diner in North America, and she tells him that she travelled the world with a tall, dark stranger (just like the eleventh Doctor, but not), but he left her in North America for another girl. The Doctor tells her about some of the adventures he shared with her that she can't remember, and Clara remarks that she feels like she went on them. The Doctor returns to the TARDIS, and sets off into time and space for more adventures, with the memory of Clara strong in his mind.
Christmas Special: The Husbands Of River Song

And that's how I would have made Series 9! It's a very long article, but I've had some great ideas for how, with some tweaking within the framework that the series was working with, we could have had a much better and more consistent season. These ideas are a work in progress, so I suspect that I'll work on them over time, and refine them to make them, hopefully, even stronger. I hope you enjoy, and comment below with your suggestions - I'd love to hear them!
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