Rambling thoughts: Plot concept for the quantum game

So you start out as an unnamed technician on one of our orbital space stations. A bearing jumps out of its track (unbeknownst to the player, this is a strike by the enemy to distort the quantum nature of space which makes it be in the wrong place.). The station starts breaking, because the rotating living quarters portion of the ship is suddenly grinding and shattering, and it's got a lot of kinetic energy which is starting to unload, stuff is moving in the wrong places, and the power plant is hit by debris from the station starting to break apart.
The player escapes the breaking station as a tutorial section on basic movement; gets to experience the simple stuff for moving, activating control panels, going through doors/drop panel things. There are no quantum effects here, and no relativistic effects.
He escapes to the dropship area, where he gets into a dropship with a bunch of other marines and lab techs. As he drops, peeking out the window he sees lances of black space spear through the atmosphere past him, knocking flying fortresses out of the air and gouging deep holes in the landscape below him. A fireball erupts in the path of a speeding cone of blue light, and the dropship is rocked by a blast. The autopilot locks onto a location - a (major?) military base - as the player blacks out.
You wake in the dropship, stirred to life by a medic. Everyone else has spread out into the military base, and he stayed behind to help you out. He pulls you to your feet, and you venture out of the dropship. Shockwaves blast you from all directions, there is massive wind, and the air is filled with smoke and fire. You glance up to see the blue sky has pulled apart in the center to reveal black space, tinged with blue to purple. Staring up, you're shocked to see an object appear. A large cylinder, criss-crossed with lines of unknown purpose or origin. A pattern of teeth decorate the bottom. It slams down, crashing through one of the dropship's wings. With a crackling noise followed by a sharp crack, the cylinder is obscured by a sphere of white light. When it is gone, the dropship has been cleanly sheared apart, and the cylinder drops down to the bottom of its brand-new crater. What seem to be stabilizing legs drop down from its sides, and it begins humming. A fireball ripples across the sky, and half a dropship tumbles through the sky towards you. You sprint away towards the only cover - the newly-crafted crater made by the strange cylinder. As you sprint for it, its humming builds in a massive crescendo, and everything goes purple. You feel excruciating pain, and the world around you, outside the space cleared out by the cylinder, is crisscrossed by cracks and lines. It shatters, and the pieces snap out of existence.
There is nothing left except for yourself and the cylinder, glowing blue lines traced over its surface. The stabilizing legs retract. You feel completely weightless, floating in this strange void.
Suddenly, you can see something in the far distance. It comes into being all around you, somehow approaching from a great distance and yet always a short ways away. You are in a hall, behind you a line of cylinders much like yours. In front of you, a cylinder bursts into being. The glowing lines on it fade, and another appears in front of it. The hall continues to fill.
A door slides open in the wall in front of the player, and he peeks a head through. The hallway is unoccupied. Red lights start flashing in the room behind him (with the cylinders) and he jumps through just before the door snaps back shut. Looking through the window, he sees the room slide down to be replaced by another just like it. Turning around, he sees his reflection in the metal wall of the hallway, and is surprised. One side of his body is covered in the same glowing blue lines as the cylinders. Staring, control is returned to the player.
[The player regains control]
Just after the player gets control, an alarm begins to blare. Whichever way the player goes, someone approaches, shouts something, and fires when he moves. When the shot hits him, remove control.
[Player loses control]
There is a shrieking rising tone and the character doubles over in pain. The aliens are horrified and run, but multicolored coruscations flood through the lines on the player's body. A shockwave shoots out, and everything goes fuzzy. Control returns to the player.
[Player regains control]
At this point the player gets to feel the quantum effects again. There are thick walls with death zones (vaccuum) beyond them. The player jitters around and, when he moves forward, can jump past the aliens blocking the way. Cutscene.
[Player loses control]
The player is seen in front of the aliens where he was before. Suddenly, he is behind them. He looks down in shock, then at the aliens in shock, then fuzzily runs away. Control's back.
[Player regains control]
Wandering around, funnel in some direction!
Finds way into laboratory!
[Player loses control!]
He finds his way into what seems to be a laboratory. The door closes, he hits a button, it locks. He's really lucky.
Looking through a door, he sees the Earth floating below. There are several other ships visible, and panels extend from each. Electric purple lines coat the panels, and they suddenly flash. A shockwave progresses around the earth and comes back, and seems to be fading out when it hits the ship you're on. Still fading, it traces along the visible parts of the ship (the room you're in juts out from the surface a bit). When it gets to you, you double over in pain. It's excruciating. More painful than anything you've ever experienced. The shockwave bounces off you, now newly strengthened. Everything gets fuzzy.

What happens next?

The aliens' star is collapsing! maybe their whole galaxy is collapsing. Maybe it's just that they're really attached to it. Point is, they need quantum effects to stop its collapse. They need extremely well-defined positions. Maybe it's a black hole headed for their planet? NO! THEY'RE TRYING TO DESTROY THE ANDROMEDA GALAXY
cancel that. They're just trying to stabilize their part of the galaxy. no?
so they've got some power generation which is granted to them by the godputer being chained up. The problem is, the power generation makes things FUZZY around it. whatever it is! It doesn't make much sense or have much justification. Point is, fuzzy bad. So they want precision so that they can live with their free power source! And that's why they're attacking.

But how do you get to attacking them? What's the basic arc?
You need to go from on your drop station to the alien homeworld to the godputer.

1 Drop station/start
2 Alien Homeworld
3 Godputer
4 End!

What else is there?
The drop station encompasses all the time from when you start New Game to when you telprot to the alien homeworld. This will presumably include the progression from solid to fuzzy to fuzzy-disrupting. So maybe this will include the travel to the alien ship attacking us!
1 Start
1a Drop Station
Learn to move
1b Earth ground!
1c Alien attack ship
This is where all the development happens.
First taste of fuzziness.
1d Teleport to alien homeworld somehow?
Maybe a power generator malfunction?
Your destruction of the generator!
You destroy the generator of the ship, which nullifies the fuzzification field!
So in this way you save the earth - BUT, you ALSO get teleported to the alien homeworld.