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In A Good Man Goes to War, Madame Kovarian said there was a war against the Doctor to which justified trying to turn River Song into a weapon against him.

In The Time of the Doctor, Trenzalore was practically a war zone between the Doctor and all those who didn't want the Time Lords to return.

Tasha Lem changed the Papal Mainframe's faith to "Silence" making them the Church of Silence (to which Madame Kovarian was a part of a renegade faction of the church) and Madame Kovarian has shown to be able to travel through time having taken River Song from 51st century and to 21st century where she placed River Song in the spacesuit to wait to kill The Doctor.

So I am wondering, does that mean that Madame Kovarian originally came from the time when when The Doctor was living on Trenzalore protecting Christmas?

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  • Another thing to consider is the war the Doctor's enemies like Kovarian and the Great Intelligence remember is something of a first timeloop Doctor who died and left a time scar and got nicknamed Valyard. But then because of all his enemies efforts he ends up in a different timeline creating a universe with Clara and NOT dying on Trenzalore. It's a paradox but it makes sense to me. It's all tangled up with how originally Gallifrey was destroyed and the Doctor died on Trenzalore. And then Gallifrey survived and the Doctor didn't die. Yet both happened.
    – lucasbachmann
    Commented Jul 21, 2021 at 22:51

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Yes, and Tasha Lem even says as much to The Doctor.

Towards the end of the episode, the second time The Doctor goes aboard the mainframe, he has a discussion with Tasha on this topic. She questions why The Doctor even came to Trenzalore, knowing the prophecies about it, and he accuses her of trying to stop him:

TASHA: Why did you ever come to Trenzalore?

DOCTOR: Well, I did come to Trenzalore, and nothing can change that now. Didn't stop you trying though, did it?

TASHA: Not me. The Kovarian Chapter broke away. They travelled back along your timeline and tried to prevent you ever reaching Trenzalore.

DOCTOR: So that's who blew up my Tardis. I thought I'd left the bath running.

TASHA: They blew up your time capsule, created the very cracks in the universe through which the Time Lords are now calling.

DOCTOR: The destiny trap. You can't change history if you're part of it.

TASHA: They engineered a psychopath to kill you.

DOCTOR: Totally married her. I'd never have made it here alive without River Song.

The term "Kovarian Chapter" would mean there was some sub-group within the Church that was led by Madam Kovarian, and that they made it their mission to go back and prevent The Doctor from making it to Trenzalnre. This must have happened after Tasha changed the name of the church to Church of the Silence, since that's what Kovarian called her group.

(There are a couple of oddities with this explanation -- like why the priests were willing to kill Kovarian in Wedding of River Song -- but nothing we couldn't use a bit of Doctor Who hand-waving to explain.)

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There is no Exact or Clear answer in the DW Canon, but it could be supposed. Also it could be from the ending of the war, living with all the devastation and those things, but i believe that it was from the moment that the Papal MainFrame fall.

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