Echoing Null's comment, it seems that you're thinking of the web-story "Goliath" by Neil Gaiman, originally found on Warner Bros' whatisthematrix.com website (as well as the subsequent Matrix Comics Vol. 1) and which features many of the elements you've mentioned:
Awakening to darkness and hearing a voice
I was standing in the puddle of the world, a weird, brightly coloured
thing that oozed and brimmed and didn't cover the tops of my brown
leather shoes (I have feet like shoeboxes. Boots have to be specially
made for me. Costs me a fortune). The puddle cast a weird light
upwards. In fiction, I think I would have refused to believe it was
happening, wonder if I'd been drugged or if I was dreaming. In
reality, hell, it had happened, and I stared up into the darkness, and
then, when nothing happened, I began to walk, splashing through the
liquid world, calling out, seeing if anyone was there.
Something flickered in front of me. "Hey," said a voice. The accent
was American, although the intonation was odd. "Hello," I said.
Their entire life was training
The next few years passed really fast. It seemed like I spent all of
them in planes of different kinds, cramped into tiny cockpits, in
seats I barely fitted, flicking switches too small for my fingers.
I got Secret clearance, then I got Noble clearance, which leaves
Secret clearance in the shade, and then I got Graceful clearance,
which the Prime Minister himself doesn't have, by which time I was
piloting flying saucers and other craft that moved with no visible
means of support.
Finally he awakens to the real world
It was like being born. It wasn't comfortable, or pleasant. It was the breathing carried me through it, through all the pain and the darkness and the bubbling in my lungs. I opened my eyes.
I was lying on a metal disk about eight feet across. I was naked, wet and surrounded by a sprawl of cables. They were retracting, moving away from me, like scared worms or nervous brightly coloured snakes.
And is immediately sent on a kamikaze mission against aliens
I never saw the aliens, if there were any aliens, but I saw their
ship. It looked like fungus or seaweed: the whole thing was organic,
an enormous glimmering thing, orbiting the moon. It looked like
something you'd see growing on a rotting log, half-submerged under the
sea. It was the size of Tasmania.
Two-hundred mile-long sticky tendrils were dragging asteroids of
various sizes behind them. It reminded me a little of the trailing
tendrils of a portuguese man o' war, that strange compound
They started throwing rocks at me as I got a couple of hundred
thousand miles away.
My fingers were activating the missile bay, aiming at a floating
nucleus, while I wondered what I was doing. I wasn't saving the world
I knew. That world was imaginary: a sequence of ones and zeroes. I was
saving a nightmare...