I… don’t get the ending…
So, Remilia, the owner of the body, loses their body and switches with the otaku Emi, who has been watching along.
And now in this chapter, how does any of this make sense? Why do both the Remilia with Emi’s mind exist and also the unchanged otaku Emi???
Who is who? Is Remilia now herself??
tl;dr: After this chapter, Remilia is Remilia and Emi is Remilia's daughter.
You seem to have missed a lot of things, but here's a summary.
Remilia got possessed by Emi as a child.
Emi built a brand new life for Remilia by hacking the game story.
When isekai Pina hacked back using cheat items, Emi was so shocked she lost consciousness and Remilia, the original, took control back.
Those were the first couple chapters, with Emi in control until the "condemnation event".
Remilia set a whole plot to fight back and reach her own happy ending.
She saved the world and got Angel on her side, then came back to the kingdom with overwhelming influence and a cure to Pina's cheat items.
All along, Emi is catatonic within Remilia and doesn't follow the events. Remilia is in control. Both still exist "within the villainess" though.
Finally, Remilia creates magic to manipulate souls.
She experiments on that with the original Star Maiden's soul who gets reincarnated as the first son of Remilia and Angel.
In this epilogue chapter, Remilia talks to Emi's soul within her and offers to reincarnate her as a second child (with nearly no memory) or a homonculus (with all memories). Emi chooses the child option.
Remilia is still in control of her own body and Emi leaves it to become Remilia's daughter.
