If you are creating a fly-around-free in outer space as if you where in an airplane game you are almost certainly bending science so far that the game is fantasy.
So make up spacey things that act as barriers. So long as they are spacey, you should be fine.
Asteroid fields so dense that you'll be destroyed going through them, with a path through it that is free of debris. Maybe that path is described through nav beacons, maybe it is kept clear by mining robots, whatever.
Or nebula. Or swarms of planets. Or space geese. Or force fields. Or lazer beams in a gravitationan nexus. Or space grues.
All science fantasy, but so are the engines of the spaceship used in every space-like game I've ever played short of KSP.
If you want technobabble (why don't see seem them now?), take whatever handwavium you use to make your engines and tie them to the new space fantasy elements.
The engines used to travel around space as if you where in an airplane (your thrusters) cause temporal anomolies / gravitational eddies / random babble. That changes the nature of space from the current "well, really, nothing here" to whatever random excuse you need to make "dense" terrain for your gameplay.
So, suppose a gravitational "knot" that has caused a asteroid belt cluster with nebula.
The 3d maze you can navigate through is the first wave. You have to go to various spots in the maze, defeat various foes. (The maze is a home for pirates, or whatever foe you want players to fight. And maybe space monsters, because that is spacey. The space monsters can have
magic gravitational powers.)
There can be parts with dense asteroid fields or whatever. Picking up navigational solutions to these swarms can let you fly through them. Or upgrading your ship with a streamlined "frictionless" surface can let you penetrate some "nebulas". Or narrow choke points defended by automated defences or "force fields" that you have to deactivate.
You could so this on a large scale. Suppose that the disaster that resulted from the activation of the experimental reactionless drive destroyed entire planets and shoved the debris into a shell, locked there by the gravitational knot. (Enough technobabble?). This was later used as weapons, destroying planet after planet. Only some planets have survived, and since then a defence has been developed. The existing shells are still out there, and civilization has taken hold in them. Navigating between them is free-space, but in them it is a set of 3d maze like paths.