Well, I'm pretty learned in the nature of Shadowrun's plot so such a thing is not difficult. It's really all about knowing which Source to read. Granted, I've read almost every sourcebook in print before 2003 which I imagine is not the case for you Pimp-boy. I've been falling behind lately, though.
I've also altered the nature of the Shadowrun contact system to allow for player influence. So a player gains influence points with an NPC which are added to dice rolls (like contact levels) but the number can change quickly based on the players actions and the personality of the NPC. The number can be negative as well, giving the NPC more dice to resist. This replaces the modifiers for NPCs being neutral, friendly, or hostile. NPCs who are highly influenced (Influence rating higher than Willpower) by PCs also change their behavior based on perceiving the PC's actions. So you could eventually turn Mr. Evil Wizard into Gandalf or drive a Shaman towards the Toxic path (though, it would be hard, because most magicians have high Willpower ratings, which are reinforced by the nature of their traditions)
The primary problem with SR3's contact system is that it doesn't allow for power levels. So instead, I simply give a number of different ratings for the NPCs abilities. Players can choose to have high-powered contacts but those contacts will always have higher rates (prices) than those that the player intentionally creates with lower stats. So if the player takes the time to "train" an NPC doctor fresh out of med-school with his money (NPCs gain Karma too, you know) his rates will stay lower for that player rather than a flash-and-chrome doctor with rating 9 Biotech who charges by the spoken word. In a sort of meta-gaming aspect, the players can force NPCs to challenge themselves and in essence improve them. This applies in reverse, whereby, the players spare their enemies so they can grow and pose a greater Threat to the players and increase their Karma as well.
