As yet there are no mods which change the story to any great degree. There are some minor tweaks, but no mods so far have had their own story.
However, I've had a look at story mission ini files in the past and I've found that they're codeable, and fairly easily too, it just takes a long time. I once created a fully functional first mission in Kusari, where you were working as Cobo for the Blood Dragons, and you had to destroy the Matsumoto in Hokkaido.
So there may yet come a day when we have our own story missions. In the meantime, if you feel you're up to the challenge of making your own, check out
my thread in the Tutorial forum. Once you've had a look at the basics in that, drop me an email (check profile) and I'll be happy to help