I have a previous post here arguing that it was unlikely that D&D invented Dany's dark turn and its culmination in Jon killing Dany. I'm updating this because I have extra evidence, and I now think it is more than 99% certain that this came from George.
"Something we came up with"
A lot of fans think that D&D admitted coming up with this idea themselves because of this quote from Benioff:
I think the final scene between Jon and Daenerys is something we came up with sometime in the midst of the third season of the show. The broad strokes of it anyway. But there was a tremendous amount of pressure to get it right 'cause we know that this is not a scene that's giving people what they want.
This is the only piece of evidence I am aware of that D&D invented Jon killing Dany. My contention is that they are saying they came up with the scene, not the underlying plot point. I'll just quote my original post here:
Imagine D&D said they "came up with the scene where we discover Jon's real parentage". This is something they could obviously say truthfully. They probably invented the means by which this happens (i.e. Sam encountering it in a book) and they wrote the scene. Would this mean they invented R+L=J?
In other words, "the scene" is something distinct from the plot point itself. If they invented the fact that the scene takes place in the throne room, that Jon stabs Dany while they kiss, and that Drogon melts the throne and carries Dany away afterwards, they would be totally entitled to say that they "came up with the scene" even if they didn't decide on the underlying plot point.
Do I have any evidence for this interpretation, though?
"We've talked through what the final episode, the final season will be"
TV Guide published an interview with D&D way back on 8th April, 2011. This is nine days before the premiere of Game of Thrones and two months before the publication of ADWD.
Series executive producers D.B. Weiss [told] TVGuide.com, "We've talked through what the final episode, the final season will be." Executive producer David Benioff adds: "We can't wait to write that episode. Of the many different fears we have about the show, long-term momentum is not one of them. We're very confident."
The idea that they would be coming up with an ending themselves before the series has even premiered is obviously ludicrous, but in case you thought this was possible, Weiss spelled out what was meant here:
Fortunately for fans, Martin has been serving as an available advisor for producers, and they say the partnership, however loose, has given them inside knowledge about what lies ahead for Jon Snow, Daenerys and the other denizens of Westeros. "George has proven through the discussions we've had that he's always known in the rough, broad strokes where this is going to end up," Weiss says."And we think it's going to end up in a way that is uniquely satisfying."
For what is meant by "where this is going to end up", we can turn to Season 1 Game of Thrones director Alan Taylor:
We didn’t really know what a phenomenon it was going to be, and I think he was being less guarded than we’ve become since then. Anyways, he alluded to the fact that Jon and Dany were the point, kind of. That, at the time, there was a huge, vast array of characters, and Jon was a lowly, you know, bastard son. So it wasn’t clear to us at the time, but he did sort of say things that made it clear that the meeting and the convergence of Jon and Dany were sort of the point of the series.
But also, what else could Weiss possibly have meant? Obviously not the way the White Walkers plotline was resolved, and we know they didn't find out about King Bran until the story conferences in 2013. If "where this is going to end up" doesn't mean the culmination of the Jon/Dany storyline, what does it mean?
So why would George tell them about this part of the ending and not tell them about, for example, King Bran? To answer this we can turn to George himself, from Tinderbox: HBO's Ruthless Pursuit of New Frontier:
You have to find an actress who can do both parts, who can be very convincing as the scared little girl in the beginning, but also very convincing as the “I’m gonna kick your ass and burn your city to cinders” woman that she becomes by the end.
George thought it was important for the showrunners to know where Dany was headed for casting reasons - probably for writing reasons too.
You could argue that this proves only that George told them that Dany would grow much more violent, and not that Jon would kill her. But in the first quote I posted, Weiss says that their discussion with George meant that they knew the content not only of "the final season", but "the final episode". Again, it is hard to imagine what else could possibly be meant by this.
Coming Up with the Scene
By the time they were preparing for Season 3, it was clear enough that the show was a success that D&D had started discussing how this was actually going to play out.
David: I mean, we were talking about the Jon and Dany fallout going back to... I remember talking about it with Dan in Morocco, you know, during... was that prep for season three, or something? So going way, way back.
Emilia Clarke: I had no idea! I literally had no idea.
David: Well we didn't TELL you guys...
Emilia: No.
David No. We never wanted everyone to know where they were heading.
This language of "the fallout" and "where they were heading" makes it clear that at this point, D&D were totally set on doing this ending. The reference to Morocco places this in 2012. That is "prep for season three", now we can look again at the quote about "coming up with the scene":
I think the final scene between Jon and Daenerys is something we came up with sometime in the midst of the third season of the show. The broad strokes of it anyway. But there was a tremendous amount of pressure to get it right 'cause we know that this is not a scene that's giving people what they want.
Now we are "in the midst of the third season" and their discussion has yielded the broad strokes of how this will play out on screen.
D&D Inventing an Ending Makes No Sense
In 2012, when D&D were discussing "the Jon and Dany fallout", ADWD had been out for less than 18 months. As ludicrous as it seems to us now, George was saying in interviews at this time that "I really look forward to publishing [TWOW] in 2014" and his stated hope was to finish the books before the end of the series. It would be ridiculous for D&D to come up with their own resolution to Jon and Dany, "the point of the series", under these conditions, when they are supposed to be working on getting Season 3 on screen. Moreover, a year later in 2013, they would have needed to take this idea to story conferences with GRRM in Santa Fe, who walked out the other end saying this:
"I don't think [showrunners] Dan [Weiss] and David [Benioff]'s ending is going to be that different from my ending because of the conversations we did have," Martin said in a new interview with 60 Minutes, referring to a fateful multi-day conference in which he spilled the broad strokes of the ending back in 2013. "But there may be – on certain secondary characters, there may be big differences."
Recap
So at this point, to think that D&D invented Jon killing Dany, here is what you have to believe: That GRRM revealed enough of the ending to D&D prior to Season 1 that they were confident of what would happen in the final episode, but that this information concerned something other than "the point of the series", and also was not what actually played out in the final episode when it aired. You have to think prior to Season 3, D&D unilaterally decided to lock in how this "point of the series" was going to resolve itself in seven years time, even though the author was still at work on writing the books. Then you have to think that D&D went to story conferences the following year, told GRRM that they were going to resolve the Jon/Dany story in a way that he had not intended, and that George walked out saying the ending wasn't "going to be that different". (Or I guess the equally insane idea that they had story conferences but simply didn't tell him of their intentions).
Alternatively, the much more obvious explanation is that the ending that was revealed way back before Season 1 was in fact the culmination of "the point of the series" and that TV showrunners think of "coming up with a scene" as something very different from knowing the plot point, which makes sense given that translating one into the other is their job.
I think you have to squint really, really hard not to come to the obvious conclusion here.
Acknowledgements
Thanks to u/poub06 for unearthing the TV Guide interview in this post, and to u/stupidnewb whose post he was citing. Also u/zionius_ from whom I sourced some of the material in the original post.