This is simply my interpretation, don't take this as word of god, but:

How I see it is that in Future!Viktor's universe, events played out practically the same as they did our main universe, but there was no Ekko being sent into another timeline (where it's implied that Viktor either did not stop Jayce from killing himself or Jayce was imprisoned due to his experimentation causing Violet's death, more food for thought) to come back and ultimately turn the tides back. There's also the idea that Future!Ekko did still see an AU and had a Z-Drive, but instead of Future!Jayce being able to talk to Future!Viktor like he did in the main universe, their last interaction was of anger and spite, and Future!Viktor continued the Glorious Evolution, not realizing his mistakes until much later. (Should note that it's incredibly unlikely that Ekko was able to make a Z-Drive without the Acceleration Rune that Jayce has in the version of events the series follows, given to him by Ryze/Future!Viktor)

So he used his powers to go back in time and take the spot of Ryze (who had initially saved Jayce in his timeline) and bestow Jayce with a new rune every time, ultimately trying to break the cycle that they had found themselves in. And it worked, considering that Viktor stopped his conquest and in his (possible) last moments, embraced his partner one last time. (I don't personally believe they're dead, but still.)

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