Basically I come up with stories through a process of creative deconstruction and "mental roleplay". The creative deconstruction is where you are experiencing some story, and you come across an event in the story that you hope turns out one way or that you think should be done differently, you deconstruct that event in your head and rewrite it, basically a form of fan fiction brainstorming, but you're just focused on the event. You can then use that event as the basis for a "mental roleplay". Basically imagine you're a kid with a bunch of toys, a couple power ranger dolls, a barbie, one of those grotesque looking Todd McFarlane monsters, a helicopter, and the upper torso of a broken GI Joe... obviously these things have nothing in common, but with random disconnected ideas, events, plots, characters, and settings you can do what the little kid in you would do, play pretend. Imagine a scenario and use everything in your creative arsenal to just throw things in and develop an event that happens, don't worry about the beginning, the end, or where this event fits, if it fits at all. The event will help give you ideas for what kind of a story you want to tell, a basic outline.
As you keep doing this, over time you get lots of disconnected events and characters... well then comes the fun part of smashing them together. Think of it like you've got a bunch of unfinished scripts for some stories, and you decide to make one super-script based off everything, You then have to decide what stays, what goes, what characters can be merged together, and amazingly a story evolves out of that. As the story evolves you can get more critical about the process.
This isn't the only or even a common method of writing stories, but it works for me so I figured I'd share it.
Another bit of advice I've taken to heart as a writer: If it feels boring to write, it'll probably be boring to read. Also don't get too attached to anything in your story. I did a lot of worldbuilding for one story before I began to flesh out the plot, and had a section where I needed my character to get from one location to another, but according to the worldbuilding I'd done they would cross a desert, I couldn't come up with anything at all interesting to occur during the desert trip, so I scrapped it entirely... the entire world reshaped and a whole desert lost because it served no real point in the story.
Don't be afraid to bounce ideas off others either, if you have the barebones of a plot, throw it out there somewhere and get some feedback, you can actually stir the creative juices by having other people give their input on a fledgling story idea.
Last of all, don't be afraid to loan out storywriting. Not everyone is a storyteller and if you can't come up with a good plot but still want to make a good game, there's plenty of writers out there willing to work with you to help develop an interesting plot for your game based off whatever basic premise you desire. Most published commercial games aren't made by one person, and their quality shows because they work as a team to bring the best elements out. I understand wanting to have complete creative control over a project is enticing but if you are truly going for quality, you will almost always need to rely on help from others. Very few of us are gifted prodigies at art, music, story, coding, mapping, etc., we all have our strengths.