Guide/GM's dont "control" NPC's in the sense you are asking about. At least for the events we're most familair with like the invasions where say named chickens kill people in Dreadlands or what not. Most GM Events are run with the GM/Guides *as* that "npc". As in they are looking threw its eyes and controlling it just like you would a player.
GM's at SoE create special characters for these guides to use and place them on the Guide's account. So like at Char Select you'd see "Jimbob_the_Warrior" and L40 or something. Then you log him in.
Then through the use of the /becomenpc command the server "flags" you as a true NPC. /becomenpc is like the #spawn command on emu in that you specify things like level limits (only Players 1-40 can hit you), texture, model, etc.
So they are really player characters that the server just "considers" an NPC through the use of /becomenpc
I'm not sure on EQEmu's ability to use /becomenpc though so i'm not sure if that is implemented
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