What kind of a 3D game? The best games (or rather: pretty much any game worth playing these days) tie their plot and story around their main mechanic. The genre and overall style also plays into this: it's obvious that a dark survival horror experience will need a radically different plot than a colorful 3D shooter with mechanics like wallrunning or rocket jumps.
In fact..."3D game" can be much more than that. Simulation and RPG's are also in 3D. As are racers. Or rhythm games. Or...
Ahem: as you can see, you'll need to be more specific. Starting with a plot isn't the best way to go about games (unless it's a text adventure game...which usually doesn't need 3D to begin with). It's better to start with a existing concept and putting it in another setting (it's like the sims...in the dark ages!), or meshing to radically different games together (it's like tetris with a portal gun).* Start with that...and if you still need a plot or idea at that point, feel free to contact me if you want.
*EDIT: come to think of it...that's what the real Jdbye mentioned. Of course you don't go LITERALLY copy-pasting stuff from those games, but it's not like ninty can sue you if you have an adventure game set in a paper-ish environment.