Maybe Agnus wasn't the one in charge of this ordeal and his jealousy led him to kill his fellow scientists and quickly grow in rank after placing blame on demons so Sanctus wouldn't be any of the wiser. Or maybe it's something even more bizarre like Arius was part of it and was later exiled for doing demonic experiments on the towns people, secretly under Sanctus command, however he was caught because he's so open about it and so they disbanded him to save their own skins. Maybe he worked on Nero first and is secret Credo and Kyrie's father/ caretaker/ uncle (etc) It would explain why Credo decided to take Nero under his house hold. My guess is he didn't show any signs of change when they first worked on him, but only recently started morph into a humanoid version of the Savior, much to their surprise. He did say his arm only recently changed. This is why I want a DMC5 and Nero to be in it. They could flesh him out and have him discover his origins that were kept secret from him. As Kyrie, she was more or less just a plot device. It give her layers would be to make him into something more than she is. It could be interesting I'll admit.