If someone pointed out to you a little boy, as innocent as could be, and you knew that boy would grow up to create the most evil the universe ever saw, would you kill that little boy and prevent that evil? Yes or No. And what would either answer make you to be? If you're The Doctor, and you're suddenly in the middle of a horridly crazy war that looked like World War I trench warfare but had biplanes shooting laser canons, and you met a scared little boy who was about to die, what would you do? You'd offer the boy a lifeline, and save him, but what if that little boy told you he was Davros and that you were on Skaro, and you knew exactly who this was because you'd fought that person and his creations (the Daleks) dozens of times before. What would The Doctor do?
The thing is we've seen the Doctor get into similar moral quandaries over the last couple years. Perhaps the Doctor is still wrestling with the Question he faced about whether to destroy Gallifrey, or to save Gallifrey?
Let's review the episodes that I'm referring to.
First - "Let's Kill Hitler" - In which Mels, a.k.a. Melody Pond, sorta kidnaps The Doctor supposedly in order to kill Adolf Hitler so that the Nazi Germany war machine would be stalled. It was actually a trap cooked up by Madame Kovarian so Mels would deliver a poison to The Doctor and kill him, in order to stop another crazy war in that case against The Doctor. But, instead of killing Adolf Hitler they just locked him up in a closet.
Second - "The Day of the Doctor" - the first multi-Doctor story of the modern era. In this story The War Doctor ("grumpy face") was dead set on destroying Gallifrey in order to stop the Time War, and to die along with all his people and at least the nightmare would be over. To do so he stole The Moment from a vault of special weapons. But the Moment had a mind of its own, and decided to put The Doctor through a spiritual test of sorts. Instead of destroying Gallifrey, all the incarnations of The Doctor together created a subterfuge where they "hid" Gallifrey instead. Instead of engaging in a massive moment of destruction, he came up with an ingenious redirection.
Third - "Genesis of the Daleks" - Even though that was aired ages ago, let's review that episode because it was directly mentioned in The Magician's Apprentice. In that episode the Time Lords sent The Doctor into Skaro at about the time Davros finished creating the Daleks. The mission was to destroy the Daleks, and indeed the Doctor did rig explosives in the Dalek mutation room and had in his hands the wires which, if touched together, would have set off the explosives and destroyed the Daleks before they could have become a menace to the entire universe. But he couldn't bring himself to do so, perhaps because of the possibility that the Daleks could be rehabilitated.
In the Magicians Apprentice we see The Doctor interacting with a much younger Davros. This Davros is scared, he's in the middle of a mine field, he's about to die, and he's been completely traumatized by the endless war his people have been fighting. Not knowing he was about to save Davros, he offers help to this little boy. But once he learned that was Davros, he simply left.
Perhaps being abandoned like that really tipped Davros over into the pure evil? So, not only did The Doctor help the Daleks at several crucial points in their history, we now know he was responsible for Davros becoming the ultimately evil raging lunatic he was?
Hoooooboy, that's a heavy piece of karma to carry around, isn't it?
How does the episode end? With the Doctor returning, having witnessed The Master (a.k.a. Missy) and Clara murdered by Daleks, and he's about to destroy Davros before Davros could become any kind of evil anything. In other words, the Doctor having witnessed Missy/Clara's murders, starts channeling The War Doctor.
Given the pattern above ... given that this was the first episode of a two-part story ... given that at the mid-point of a Doctor Who story all hell is supposed to break loose, only to be resolved later in the story ... do we believe that The Doctor will follow through on the plan to destroy Davros?
I kind of think next weeks episode won't follow through with DESTRUCTION but will somehow take a different path. But what would that path be?
Another question :- Even if The Doctor does kill Davros, who's to say someone else in the Kaled race won't do the same sort of thing Davros did? The Kaleds and the Thals have been locked in a thousand year war of horrendous proportion, and surely everyone is completely traumatized. Traumatized people tend to become torturers, and the deeper the traumatization the deeper the evil the people are willing to commit. Maybe just maybe someone else among the Kaleds might have been just as brilliant a scientist and just as deeply damaged as Davros and just as willing to commit utter evil?
Another question :- At what point of the timeline does The Doctor return to destroy Davros? Did this follow or precede the murder of Missy and Clara? How did he return to that point of time if the TARDIS had been destroyed? It's possible this followed the Missy/Clara murders, and that Davros had some kind of time travel device to let the Doctor travel back and do the deed. In which case, is Davros feeling regret over what he'd done with his life and hopes to rewrite history so he never did those things?