Are you using the main game as a dependency? IF you are, you should give the NPCs an alignment that's hostile to the players. For example "Evil NPC". You can do this in the sidebar of the tool.
If it's from scratch. I think you can just copy the alignment file from the main campaign. You can find it at /Data/Mods/Main/Story/Alignments/
It's just a text file you can edit. Make sure your relations are setup correctly. 50 is neutral, 100 is friendly, 0 is hostile.