How can you create an original video game plot?

First, we need to work on your terminology. The plot is the main structure of a story. Some games have stories, some don't. You listed Fighting, Platforming, Shooting -- those are game genres. Genres are subsets of an artform based on similar characteristics. Super-hero comics, horror movies, strategy games, classic rock music -- these are all genres. So if you are saying all the genres have been taken, I'm not sure that it's true, but even if it is doing something new within a genre or combining two genres in a new way is just as good. Create a 3D platform shooter. Or a horror RTS. There are lots of untapped choices still to go.

Keep in mind, back around 1900 some high-level guy in the US Patent Office said they might as well shut down the office since everything that could possibly be invented had been. He couldn't see what possibly was left to make. I think we've come up with a few ideas since 1900. I'm also sure there are more game mechanics and game genres to be discovered.