Once you beat her, Eve's surprised at how strong Fran, who she calls "Nee-sama", is and decides that she's (Eve) incomplete. But before you could continue, a mysterious voice calls Eve back saying that they have enough samples to work with. Fran recognizes the voice and Eve calls the voice "Otou-sama" and follows orders by escaping using Blasted Tree (Fran's NP) as cover.
In the second interlude you decide to go with Fran to hunt down Eve, who Roman dubs "E-Fran." E for "Enemy" and I'm not 100% sure but Fran seems reluctant to see Eve as a sister. During the hunt you face more Homonculus which Fran attacks in a rage.
Once you beat them, Victor Frankenstien shows himself, but his Sprite is just a standard cloak surrounded by shadows. Roman realizes that in this Singularity, Victor Frankenstien was still alive somehow even if in such a state.
Eve shows up and asks if it's okay to fight and Victor says, "Go ahead, Eve," naming her which shocks Fran and he explains that he took the name from "Adam and Eve"
And Eve goes all happy that she gets to kill her sister.
"Un, un, un! I'll do it! I'll do it! Will kill Nee-san, I will, I will!"
"...uu."
Fran just groans in response and Victor starts insulting her lack of speech when she then goes "Shut...up" which blows his fucking mind apparently.
"Talking...is tiring. But this once, I will. Chichiue, Imoto. Your time, ended, long ago. I found, my own, friends. I chose, my own name. That's why. Together...let's..."
But Victor and Eve refuse to listen anymore and attack with Mashu saying that we'll help Fran.
The find ends with Fran exhausted and Eve beaten. Eve refuses to accept defeat but cowers when Fran let's out a long scream at her and smacks her.
Victor: For goodness's sake...(Yare yare)
Eve: O-tousama, Otou-sama, otou-sama, no good, no good, no good, too strong, scary, scary!
Eve breaks down as Victor looks on exasperated. Victor then goes on to say that she was just a tool before he stabs her.
Eve: Why? Everything, was, for, Otou-sama's, sake.
Victor then goes on about how he needs a body and goes and takes Eve's body and her power as Eve begs him not to and that she just wanted his love and praise before she gets possessed fully, and Victor's half-assed sprite vanishes and Eve's becomes a Shadow Fran sprite.
He then removes Eve's limiter to fight you, but of course, since he's still Fran, Berserker enemies can get beaten down so easily...
Even after his defeat, Victor refuses to accept his death and disappears with a whimper.
With that, you prepare to head back to Chaldea Fran has some more words for you.
"Master, is, the best. History, the world, we'll save it. ...Will do our best!"