Just like the title says, I want to discuss the relationship with both characters. See, if you think about, Vergil and Rookie have an interesting relationship, if you get all the audiophiles. Vergil leads Rookie where to go, helping throughout the city, while Rookie learns Vergil's past. Vergil is following his programming, and that is the to protect, but he evolves and at the end is willing to save everyone if you listen to the files. And by doing this the person he protects is saved, and so he begins to protect Rookie. Rookie depends on Vergil and so a relationship similar but different to Chief and Cortana's relationship is formed. Rookie learns more of the truth of New Mombassa, and at end, understands and trusts Vergil.
Vergil gives him weapons because of the Audiophiles, but lets look at it differently. Lets say that every time Rookie wastes time to learn about New Mombassa, Vergil trusts Rookie more. So when Vergil gives Rookie weapons and mongeese, It means he trusts you. And then at the second to last level, he warns you of the corrupt cop. He is actively trying to warn you, which shows he cares about you.
What I'm trying to say is that both characters end up quite different than they did at the beginning, and I'm surprised no one has discussed this subtle relationship.
I think both characters have subtle development as the game goes, but I never seen a lot analysis. SO tell me what you think!
On a side note, if a sequel occured, would you want Vergil and Rookie to have the same type of relationship, teaming up to survive?
[Edited on 10.27.2012 6:22 PM PDT]