Miquella the brat
Lol I wish Malenia came flying out of nowhere to save the day! 😭
Tbh, I have a headcanon about something similar.
Malenia, being Miquella's twin and also an Empyrean, is immune to her brother's bewitching/charming ability. She is also aware of when it happens or has happened to others, recognizing the signs, sensing her brother's powers at work and knowing Miquella's motives/personality well enough to discern the truth.
For that reason she tries to nip this behavior in the bud by either talking Miq out of it, finding an alternative way for whatever he is planning or flat out requesting he stop this.
Now, thanks to SOTE's ending, it's become rather evident that Miquella is a extremely morally grey person. He's not evil but he is an anti-villian— an antagonist who does bad things for the right reasons (I love this trope so much but it took me a while to realize Miq fit this trope perfectly).
He doesn't want to hurt anyone or cause pain- which why he just removes that possibility by bewitching his "allies" and being kind to everyone he crosses paths with (I don't think he charms everyone he meets but he does probably play up the "Kindly Miquella" persona, which is still part of his real personality, however if all else fails, he brings out the big guns and *KABLAM* you've been brainwashed). He wants so badly to create this perfect future of his, that he resorts to the "by any means necessary" that many typical anti-villains perpetuate (think Magneto from X-Men, Gellert Grindelwald from Fantastic Beasts and Jinx from Arcane). Despite Miquella's lofty dream of this wonderful future and new age, his way of achieving it is definitely suspect and morally wrong.
Malenia knows this and she is aware of the lengths her brother will go to accomplish his goals.
This could be why Miquella left her out of his plan involving godhood and the Land of Shadow.
He knows she'd disapprove or try to stop him (not physically but to talk him down or reason with him and at this point, I think Miquella has no intention of being "reasoned" with). He's desperate for this to go off without a hitch because this plan has likely been several centuries in the making. So he leaves his sister out of it, likely resolving to return to her after it is all said and done. With his new status as a god perhaps there is a greater chance of curing Malenia's rotting sickness. Malenia would only get in the way despite his intention to cure her ("I wanted your help but not like this" vibes) and he doesn't want her to get hurt anymore for his sake (it is probable that he's painfully aware of what state his sister is in and knows she's mentally compromised). Unfortunately for him, he wouldn't be able to charm or bewitch her into sitting on the sidelines even if it was just with her health and condition in mind and not the getting-in-his-way part.
In this event, it is probable that before Malenia and Radahn fought each other to a standstill in Caelid, Miquella gave Finlay instructions that if and when his sister became compromised (aka blooms into Aeonia), to take her to the Haligtree and keep her there. Miquella is hoping Malenia will be protected there but also unable to stop him from carrying out his plans.
Everything falls into place, Mohg "steals" Miquella away, he makes it into the Land of Shadow and begins his journey with Malenia none the wiser, using his bewitching ability to secure his allies without anyone to stop him.
He always planned to go back for his sister and in the last battle when he's defeated, it probably occurs to him that Malenia's fate is sealed with his death. She'll never be cured and she'll die waiting for him, having depended on a lie to keep her going just like everyone else in Elphael.
Personally I'd like to think one of the biggest reasons for Miquella's transition into that of an antagonist is because of Malenia. That his determination to achieve godhood was centered around trying to cure his sister (and perhaps find a way to help Godwyn as well).
I mean, his whole personality and plan revolve around helping people even if they don't want to be helped (in the bewitching case, forcibly so).
Miquella leaving Malenia behind is also very similar to his discarding of St. Trina. She knows Miquella can't be allowed to achieve godhood and she also likely knows (just like Malenia) that his methods are wrong and would only come back to bite him later. Malenia wouldn't want this, St. Trina doesn't want this but both of them love and understand Miquella all the same— they are two people who love him so much, they have to stop him.
Over all, Miquella really is the perfect anti-villian... benevolent in his goals but his methods are morally wrong.
Miquella has to be stopped by someone regardless of his reasoning and his altruistic goals. He's desperate and very alone (sorely lacking real allies and friends who aren't bewitched). With his twin sister and other-half safely out of the way (that's very important— that they are safe, seemingly awaiting his return), it falls to our Tarnished to stop him.
I don't want to undo his anti-villian arc but I do wish there had been some sort of saving grace moment in the final battle instead of more slaughter. Perhaps a way to cure Malenia is given to us by Miquella or even some additional dialogue from him explaining his reasoning further so it is flat out established that he's not evil, just very misguided, so the player feels conflicted for killing him and Radahn. It would've at least saved him from getting labeled "evil" by everyone who isn't a Miquella fan.
Anyway, thank you for coming to my TED talk about why Miquella left Malenia behind! 🙂🥲