Who cares? probably no-one. but, I want to at least have the details out there, so even though the mod is dead, it is not dead in total mystery. the mod was about exploring all of aperture, so I find it only fitting that I reveal the entire story when it's dead.
It is a long, LONG post. there was quite a story planned. Also, this is an ancient story. if I could retry it, I would probably revise next to all of it. but I felt putting the base story on here would be best.
The player would be introduced to test chambers, run by humans. The tests would end without death, and with some form of cake reward. during the tests, you'd keep getting hints of something running around the tests. Like in the bonus map, tendrils and eyes would follow the player in bts scenes they'd encounter.
This was part 1, and I wasn't quite sure how to introduce the segwey to part 2.
there was to be a freeroam mode too. to take an example, in most Lara Croft games, you can explore the mansion at your leisure. this would also be the case in the mod. you could explore the entire facility, and unravel more plot points.
the facility was to be protected by an illusionary holographic system that, in short, cloaked the facility to look like barren wastelands. Outside of it was to be old, abandoned homes for Aperture staff, lost to zombies.
the facility, over the years, had evolved to use it's space for more arbitrary reasons. some given up to nurseries, some to offices maintaining human history, and even some dedicated to in-house entertainment, for tv show sets.
I was going to have one of the events be Breen, teleporting from the broken teleporter scene. he would discover the undisturbed haven, and betray them to the combine. As they were so secluded, they had no knowledge of breen's position, allowing him to roam free. This starts part 2.
Part 2 was to start in your own room, where you awake from sleep to alarms and chaos. zombies have spilled in, the shield system has been sabotaged (presumably by Breen), and combine are also attempting to take control.
You venture through the facility, level by lever from the main hubs. You'd start off with closed-corridoor environments and zombies. in time, you'd discover a nursery section, and there would be specialized child zombies. perhaps a bit controversial, but we wanted to aim for a realistic setting, and it seemed to just click.
Some special events, such as the combine breaking through into one of the hub rooms, and trying to hold the security room from zombies on one side, and combine from the other.
after a long while of moving through these closed spaces, you'd encounter a GLaDOS system. with a horde close on your tail, she would open up a panel that would take you deeper behind the facility, trying to keep you safe.
You'd come to a large, bottomless-pit room with a large catwalk, leading to the far end of the room. at the far end would be a humanoid figure inside of a glass tube, with tendrils connecting it to the machinery. it's eyes would be green cat-eyes, which is what I had put into my custom maps. it's skin would be black all over, with green circuitry all over it. It was actually concepted from a still alive remix (I think it was a "dj spaz" remix.).
This was the "Genetic Lifeform" component. I always found it odd that GLaDOS was all machine, and not organic. this would be the organic part of her.
upon approaching her, a strider would break into the chamber from the side, and shoot out some of the machinery. Then, upon attempting to step into the room, would trip into the bottomless pit, taking out the catwalk.
the next bit would become an escape/testing section. chased by advisors, you enter a series of test chambers. you have to solve them fast, while the advisors attempt to break into your room. the GL unit would now be mobile on a train-track compartment next to the chamber, attempting to get the doors open, but needing the tests to be completed in order to do so.
After about 5 of these tests, you would get to a shuttle system, that connected to a underwater aperture lab. the fate of the GL would be unknown.
you would progress through these labs in much more organic environments, with little threats. the combine would break into the lab eventually, and you'd be trying to outrun/gun them towards the end of the facility, where another GL unit resides. upon helping her escape, she would place you in a teleporter to a safe haven. as you watch her pod escape from beyond a glass window, combine would break into the room, and attempt to destroy the machinery, causing your teleport to malfunction.
You would wind up in the bowels of an buried temple, and have to portal your way out, avoiding ancient traps etc.
Upon reaching the top, you'd need to take out two androids, and then, get to a driving section.
I had not planned this section, but eventually, you'd arrive at the abandoned aperture town. fighting through the town, you'd encounter the house where you lived, and a flashback to the beginning of the combine invasion would happen. you'd be a baby, held by your parents, fleeing the town to Aperture, followed closely by fast zombies. One by one, the family would be picked off, until the mother throws you beyond the protextive shields of Aperture.
Upon fighting back into Aperture, you'd encounter a stronger combine presence, and fight to the bottom of the facility, wherein, you would get to a portal-storage section. basically, a quick-move hub. the only activated one leads to Black Mesa. you'd go in, and walk through the eerie dilapidated innards of Black Mesa, post-destruction.
you'd find the entrance catwalk to the facility now filled with dirt, with a tunnel leading upwards. after puzzling through the caves, you'd exit to a large volcano, with an aperture entrance to it, protected by combine. through battling combine through this facility, you'd come to learn the GL of this facility sold out all other aperture bases, in exchange for technological superiority and more power. it'd lead up to a large battle with the GL, using portals to redirect lava flows onto the GL. during the battle, the lava begins erupting, and the stage starts to float upwards through the volcano. after defeating the GL unit, you'd be stranded on the island. a nearby pipe hatch would open, and you'd then escape into the tube.
The end of the game would pan over all the apertures in their destructed state, show the GLs that escaped in their pods connecting to an unknown icy facility, and a jumpsuit floating in lava from the now-erupting volcano. the camera would then pan onto crates of jumpsuits tipped over, implying that the first was just one of them, and the character escaped intact.
In hindsight, for one game, this would be far too huge a plot. but, this was my aspiration. a lofty goal, and the plot is far from perfect, but that was the initial story I planned.
I hope it's at least offered a window into my idea for everyone, as well as be the final nail in the coffin. for a while, a part of me wanted to save the plot, just in case. but, frankly, I don't want to leave any loose ends. this is the last one, and after this, I feel I can leave it all behind happily. 
