Based on the world of the games and the books, the one that feels most canonical is Ciri becoming Empress. That's not a bad ending though, it's more bittersweet. For starters, Ciri is a good Empress and probably leads a prosperous time for her kingdom. Not only that, she didn't die from The White Frost. So, she goes on to become a good queen to her people using the knowledge and wisdom that her true parents, Yennefer and Geralt and Vesemir, taught her.
Also no matter what, none of the games are canon. The games do a great job of taking inspiration from the books and referencing them and setting up a scenario like the players are getting a proper continuation and conclusion to the books. But no matter what, the conclusion is what the author says it is. And if he says the games are not canon, they aren't canon. The games are their own thing and all their scenarios are basically separate AU.
Also, the Signs are not alchemy. They are simple magic spells the Witchers learn in their arts. The Witchers are not powerful magic casters like sorcerers and mages, but they are able to conjure the lower-level signs to help them do their work.
The Signs are basically small little magic spells. They are done using the finger symbols and concentration. This is taken from Blood of Elves:
...The witchers adapted the spell, making use of the fact that it does not require knowledge of a magical formula — concentration and the hand gesture are enough. That's why they call it a Sign.
Alchemy is decidedly different. It's transmutation of something into something new.
There's nothing wrong with Ciri becomes a Witcher ending. OK, she didn't get the Trials of Grasses, but for the sake of the games and for all intents and purposes, she's basically an unofficial Witcher but a Witcher nonetheless. It's an ending in the game, and it's a decent enough ending. I don't think it's the best ending because I think it's really better for everyone that Ciri ascends to the throne even if it means she can't be with Geralt and Yennefer. Regardless, it's better for the kingdom and all its citizens that she is queen, and Geralt and Yennefer could still visit her anyway when they take breaks from where ever they ended up.
In Blood and Wine, the game ends with Geralt getting his own place. If players went after their favorite lady, they get to settle down with her. The rule of the Witchers is that they never die in their own bed. But in the games, the time of the Witchers is ending. And it seems Geralt is able to settle down for a quiet, peaceful life, depending on how they play.
That's why I love Witcher 3. No matter what anyone says, there's no one way to play the game. IMHO there is no true canon ending. Or rather, the true ending is whatever the player wants it to be. If they want Geralt to be with someone, he can be with someone. If they want Geralt to reject both women, he can. If he tries to get them both, he will get rejected by them. Geralt might be too over-protective of Ciri and cause her own doom inadvertently. Or Geralt can encourage her to become a great leader or even a Witcher by trade. The player's play style determines what ultimately happens. There's no one or proper way.
The only true proper way when you get down to it is what the creator says is law. So don't worry about that and just have fun with the games.
If they really wanted to, CD Projekt RED could do a Ciri only game. Honestly, I'd rather use what they built for Witcher 3 and make some completely new dark fantasy adventure.
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PCGN
