So, I've found this dialogue. It appears as if Vergil was supposed to have been killed by Mundus during the boss battle.
IGV_1446=Dante - Do Something! IGV_1447=Look there, inside, we've exposed him! IGV_1448=Yeah, I see it. IGV_1449=Avoid attacks, stay alive. Easy! IGV_1450=Come on Vergil ! IGV_1451=Get a move on Vergil! IGV_1452=AAARGH!! You!!! You killed my child!! Raaaa! IGV_1453=Dante - I need help here - slow him down! IGV_1455=Now Dante, get to the eye! IGV_1456=We need to get in there, and kill him. IGV_1457=Noooooooo! IGV_1458=You killed my child, I killed your brother. Now we are even!
And also this.
IGV_0829=What have you done to him? IGV_0830=I have killed him, just like I killed your mother. IGV_0831=****! IGV_0832=I am Nephilim Mundus! I can kill you! IGV_0833=I have slain an entire race of Nephilim, and you will be the last! IGV_0836=Burn! IGV_0837=That's for my mom! IGV_0838=For Vergil! IGV_0839=And for ******* with me!
--- A warning to you both - choose to follow me or oppose me and I will kill you.