Dark Souls: Already kinda the case
Magic: The Gathering: Bolas kills all the Neowalkers minus maybe Ugin, then he and Phyrexia conquer the multiverse.
Bloodborne: Also mostly the same
Berserk (Verse): The series would have ended before the Eclipse could even happen, since Zodd would have killed Guts and Griffith.
Cthulhu Mythos: This basically just affects Nyar
Darkest Dungeo: Honestly, not much changes. The really scary stuff like the Sleeper and the Heart of Darkness are specifically killed before they can get dangerous, and the HoD apparently wins in the future anyways. A Vulf raid week one would be terrible though.
Destiny: Depends who is considered an antagonist. The most likely survivors I see are Oryx and his court, Rasputin, Osiris, Eris, Callus, and possibly the Player Character. If we take the Darkness itself into consideration, then as of now rip verse. Even Rasputin realized the only possible way to survive against the Darkness was to emulate it.
Warhammer 40,000: If this means that the Chaos Gods get their shit together and stop infighting, canonically the emperor can't hold them back anymore and Ynnead will never form. It's outright stated that the only thing holding them back at this point is their contradictory nature and themselves. Though then again, Tzeentch doesn't actually want to win, as that means an unchanging state, so depends on what you consider Bloodlusted.
Salt and Sanctuary: Pretty much the same
Hotline Miami: Pretty much the same
Hollow Knight (Verse): Basically the same
Super Smash Bros.: I guess this just means that the hands get bored of playing and do something else? idk
The Legend of Zelda: Well, Ganondorf's an even bigger issue now
DOOM: Basically the same