The answer is simple, you're wanting a hold your hand game that has a plot, and a final boss. I'm not saying that's a bad thing. It's just, Kenshi isn't a hold your hand game. It's a sandbox game with ninjas/samurai. And what you're describing is better found in Bethesda's games.
I know you might not like that, but this game isn't for you. Dark Souls has a plot, Mario Bros has a plot. however, Kenshi is an elaborate Lego game with simplified pieces. If you want to build up a squad of super solders and destroy a town you can. If you want to have a Harem of women at your disposal then you can. If you want to mod the heck out of this game to do pretty much anything you want... you guessed it. you can. but a major plot it does not have, and if making your own plots for the game isn't your desire than I don't know what to tell you.
I can't make you like a game that has no plot, but has so much to offer in the way of personal story telling.
I honestly have turned some of my friends away from playing this game because I knew they didn't have the personality to play it. Some gamers are balls to the walls completionist, and others are chill and thrill players. once again there's nothing wrong with either type of gamers, but it can get frustrating when a person buys a game that doesn't fit their playstyle but has a cool concept.
Know this. I use to be a completionist in games, but as I've grown older I've just found goofing off in games to be more relaxing. maybe that's the reason I like Kenshi. I can just mess around for hours doing stupid crap in a pseudo world of my design. Without the hassle of a game timer telling me I have to get something done before the time runs out.
Who knows, Kenshi 2 might have what you want, but from what I've seen as far as its development it's going to be just a better version of the first Kenshi.
Hopefully this answers something for you.