three-dimensional is a bit of a misnomer. All space travel is orbital (all of it). You're either in a stable orbit around a planet, or you're taking a hyberbolic orbit to launch out for Mars (during which travel you orbit the sun), etc etc etc. The star-wars-esque giant dogfight battles look *awesome* and they're way more fun to imagine and write, but that's not really.... how....

Alright, let's say the Drej are attacking Earth, and we want to fly up and play defense. To approach the planet, the Drej will have to enter a stable earth orbit; to do that, they'll do a hard burn to decelerate and then pass *extremely* close to the planet to bleed off excess energy via atmospheric friction, resembling a [url=http://en.wikipedia.org/wiki/Molniya_orbit]Molniya orbit[/url] There is a brief (as in, minutes-long) window during which an intercept is possible, but the speed and energy of the Drej ship is ridiculously high compared to what we can achieve -- think, trying to chase down a jet fighter on foot -- if you were in the right place at the right time, you might have a chance to squeeze off a shot or two, but you're not getting into a firefight. 

[img]http://1.bp.blogspot.com/-de8S_7biOIY/Tp74FopKaQI/AAAAAAAAATg/XDArVuURjZ0/s320/per.bmp[/img]

So let's assume they make their pass and settle into a deep orbit around earth. Why deep? It's by far the most advantageous -- you maintain a high amount of potential energy, which is much more sustainable than kinetic (kinetic energy is decayed by friction). That's not to say that they don't have kinetic energy, too -- they certainly can and probably would, since interplanetary or interstellar travel requires a tremendous amount of energy. They're screaming around our planet at high speed and at great distance. To fight them we have to reach their orbit; meanwhile the Drej can throw a coke bottle out the window and it'll strike us with the force of a meteor. 

[img]http://www.scientificgamer.com/blog/wp-content/uploads/2012/02/geosynchronous-orbit.jpg[/img]

But let's say that despite that monumental (insurmountable?) disadvantage, we're still somehow able to elevate some forces up and fight the Drej in space. We reach their orbit and... oh, wait, did we? They've calculated our trajectory, and used a short fuel burn to change their orbit. Now they're in a different orbital plane from our intercepting force, which limits us to precisely two opportunities for engagement per rotation about the earth -- and then, only if the timing is perfect, and the Drej pass these intersections at the same time we do (assuming that our orbital paths cross at all, which, they may not do)

[img]http://satelliteorbitdetermination.com/Orb_elem.gif[/img]

But hey, humans are smart. Let's say we out-math the Drej. We manage to manipulate our orbits faster than they can avoid us and, closing in from behind, our interceptor gets into a firing position. WIN! He fires and.... well, shit, suddenly he's plummeting back to earth! What just happened -- well, Newton's Second Law. See if you fired a bullet in space the natural thinking is 'you go backwards,' but that's not entirely accurate. You're carrying energy, kinetic and potential, which is what defines your orbit. When you fired from that orbit, you traded energy with your bullet; it goes faster and you go slower. Unfortunately in this case, that means the bullet's trajectory becomes LESS eccentric (more circular), and your orbit becomes MORE eccentric (a flatter oval). That means you fall screaming to earth, while the bullet sails wildly off into space, and the Drej just keep on orbiting!

[img]http://f3.thejournal.ie/media/2013/10/whoops-3.gif[/img]

So, long story short, there's a reason it takes a few billion dollars' worth of manpower and computing equipment to rendezvous a shuttle with the ISS.