This mod from rgggclp allows you to give oders to your faction and they will follow them. This is just a patch, you need version 2.5 installed for this to work.
Author: rgggclp
Readme File:
You need to install Faction Commander 2.5 first!!!!
Fix various bugs in the story line mode:
* Main quest of Duty officer at the entrence of Agroprom.
* Side quest of Stalker scientific group at the swamp of Agroprom.
* Main quest of Stalker messenger at the lagoon of Garbage. (haven't tested it yet, sorry)
* some other side quests that I don't have time to test...
v2.5 is found here
Moddb.com