In a roundabout way Nicodemus is not the bad guy we all know him to be.

My theory starts with the outsiders trying to break in to our universe. Imagine if you will Lucifer an angel in heaven who wishes to act and repel the invaders but God himself does not act because "God moves in mysterious ways". He then decides to rebel against God after seeing how much of a danger they are. This all falls apart and he's cast from heaven along with the other fallen but he wishes to carry on the mission but now can do it without the blessings of heaven. He sends the fallen out to gain allies or bodies to carry on his work. One of them is Nicodemus Archleone, who is probably aware of the outsiders and its this that allows him to remain the controlling party in their partnership.

Over the years he begins a bloody conquest to destroy those Nfected and agents of the outsiders. The brilliance of his plan is that to everyone else such as Harry what he is doing is just evil and wrong, when actually he is covering it up so "the enemy" as he later says to Deidre wont discover them. Spreading the plague weakens humanity and wipes out Nfected, acquiring Ivy is a more calculated move to directly target the Nfected, stealing the weapons from Hades furthers that goal, Nicodemus is likely aware of what Harry is and so seeks to recruit him:

"A great deal of work needs to be done, and not all of it repugnant to you. In fact, I should imagine that some it would prove to be quite satisfying to your personal sense of right and wrong". Thats because in a desperate, drastic and frankly damning way Nicodemus is trying to save the world and Harry would be a great help to him