Alright, I'm gonna take some wild swings here:
The villainess is someone who succeeded in doing what the sister tried to do: transport herself into the game, however, she ended up the villainess instead of the protag, so she's trying to steal the right to make it back home. The fact that she's the only one who realized something is up makes me think she's from outside the game.
After a few interactions (or, in the case that the author wants to/is told to drag it out for money, many, many interactions), they're both gonna find out that the other is also stuck, and work together to try to find a way that both of them can return home. As they're doing that, they start building a romance to the disdain of the "capture targets" (and his sister who has to watch her brother be flirty with someone right in front of her salad. Not in a brocon jealousy way though, just in a... ew kinda way).
After they finally find a way out for both of them, they meet up in the real world SAO style except this time without 24 episodes of bullshit distractions and an atrociously handled rape scene.
Also bonus points if, when they make it back to the real world, the villainess girl is just a normal girl instead of the "hot anime girl template" girl that the villainess in game is. It'd be pretty dumb to take a manga like this that is pretty clearly making fun of "anime hot person" tropes (i.e. every capture target looking pretty much the exact same with different hair slapped on them) to go on and make the romance target for the MC into one of those exact tropes it's parodying.