I found the answer to this on this forum. I forget who posted it. If you create a standalone mod you need to do 1 of 2 things.
I could be slightly wrong on the details, but either set the alignment of the NPC you want to fight you as "0"
OR
set it to whatever alignment you want, such as "Evil NPC", but you have to copy over the Alignment file or folder from the main and put it into the corresponding directory in your mod's file location. I'm trying to find the forum post I found the solution on, but a quick search for "combat" or "alignment" is not yielding me the post. So fiddle with what I said or scour the forum, because the solution is in one of those posts. I'm not home right now so I can't look at the specific file location that I had to move.
I believe, essentially, the game doesn't know that Evil NPC and Hero Player1 or whatever your alignments are hate each other unless you provide the information with an alignments file. They actually have various levels of attitudes toward each other and so you can pick alignments based on this. An example is, you might not want a friendly AE spell to cause your friend to turn against you. So the proper alignments are important.
This was definitely breezed over in the tutorial videos, along with almost every other detail about how to get things to actually work.
Hope this helps! Sorry if it's vague and possibly incorrect.
