Reading up on “Branch E”, as the Side Story Novel seems to have been dubbed. It seems the fandom has actually been misinterpreting Two’s catatonic state this whole time. Not that that’s anyone’s fault, since this is only explained in the 5th branch.
It implies that at some point in the final chapter of Two’s DLC chapter – most likely after the homunculus fight starts –, the player is actually controlling Two as taken over by the Flower.Â
The corrupted and mutated soldiers and children send Two into such a state of shock that she is unable to fight, and so the Flower takes her over.Â
After the fight, she falls under the catatonic spell we all know and hopefully don’t love. We’ve always assumed that this is a “mind break” of sorts from the incident at the orphanage, but the novel confirms, that at least in this 5th branch, that it was voluntary.Â
Two became aware of the Flower, and so she retreated into herself of her own volition so she could fight her own power. Her odd behavior, such as refusing food, was done because she felt that if she weakened herself, she would in turn weaken the Flower’s influence.Â
This implies that the Flower actually took Two over long before the other girls, because its hold on her never completely breaks after this point except for in a brief instance that I’ll get to. But she seems to retain her sense of self and the willpower to voluntarily shut herself down to try to impede the Flower’s influence.
In the midst of it all, she strongly desires to speak to Cent, which actually briefly neutralizes the Flower’s hold on her. She tells him not to blame himself, and explains that the Orphanage Incident is not the main cause of the state that she’s in and that she needed to lock herself in herself in her attempt to combat her own power. She’s losing that fight, and so she asks him to do two things. She asks him to kill her, and for him to survive. She smiles at him before succumbing again to the Flower.Â
This explains why she is absent from Branch D as well, and why before his regression to a dove Cent talks as if she were already dead.
Disclaimer that I’m not 100% fluent and so some details might be a little off,  but I believe this is about the jist of it!
