In JK (not MOTS) I'm trying to add a character who is on your side, as a test I took the stsentry.ai file, copied it to a misc\ai\ subdirectory in my project directory, and changed the alignment from -1.0 to 1.0. To my understanding this should take any stormtrooper that I give this AI to shoot at any other stormtroopers and not at me. However when I try it the ST fires at me and ignores any other enemies around. I've tried the friendly cog but it doesn't achieve the desired effect since 'real' enemies ignore the friendly one and the friendly one will fire at civilians. So my question: is there any way to get this to work in JK or do I have to go to MOTS?

This stuff is one of the better improvements in MotS. You can kinda do this in JK, but the baddies won't attack your sidekick.
Open his AI file, and change his alignment to 1. That just stops him from attacking you. You'll have to use a cog for anything else.

In MotS (I just posted this in another thread ), Change the alignment to 1. For your sidekick and all enemies, open their AI files, and change LookForTarget to LookForOpposingTarget. It works pretty good. You're still the top priority kill, but they will shoot at your sidekick, and vice versa.

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