You know, I was sitting here just thinking, and thought I'd give a retrospective on what the story exactly is, for those who got lost along the way.

The story can be presumed to take place in an alternate version of Aperture, where events took place in such a manner to where everything in the facility here that contradicts the main story of Portal could have happened.

You play as a male test subject known as Mark Bendest. (In the previous version of the story present in the original maps, this character's story was emphasized, whereas here it is not. But, long tale short, Mark is a subject who volunteered for an experimental test in which he visually transformed into the shape we all know as Bendy, the Aperture Science stick figure. This story point is a moot point now, and can be ignored.)

Wheatley is up to his usual story action of trying to escape the facility; and he needs a test subject to help him do that. Unbeknownst to him, GLaDOS is actually keeping a close eye on him. Subtly helping him in actions he believed to have achieved by himself, all in order to lure him back to her chamber. So, as it goes, Wheatley goes to a nearby docking station and recalls a relaxation vault; the very one containing Mark, AKA the player. After retrieving the player from stasis, Wheatley then makes a move to unlock the main elevator shaft so that he and the player can use it to leave. Heading to a control room outside the factory and using it to unlock the elevator shaft, the player and Wheatley then take a brief detour past the neurotoxin generator, where Wheatley recalls a tale of when he was the assistant to the one responsible for maintaining the generator. His actions got the button removed from the room, and a store of Neurotoxin can be seen clogged under the generator.

Reaching the elevator and having the player plug him in on a conveniently-available rail mount, he attempts to hack the elevator to send it upwards to freedom; his plan apparently fails when it heads straight in the opposite direction, down to the lowest point of the shaft accessible; the rest of it below is flooded. This unfortunately lands the player in front of the Central AI access; Wheatley can't leave without the player's help, so he makes his way down the rail and tells the player they need to pass through GLaDOS' chamber to find another way back up, as the only other door accessible on this floor is rusted shut.

Entering GLaDOS' chamber, she apparently seems to be turned off or else asleep when the player enters with Wheatley in tow. Heading across to the button visible across the way, GLaDOS suddenly awakes with a laugh and seals the player into the chamber. She mocks Wheatley for falling for her trap and then attempts to gas the player with neurotoxin; the plan fails, as there is no neurotoxin immediately available, calling back to Wheatley's past mishap with the neurotoxin generator. The Announcer then denounces GLaDOS as corrupt for her attempted re-pumping of the neurotoxin. A core transfer ensues, but before Wheatley can punch the player into a pit, the facility begins to go into meltdown sequence, and GLaDOS' head is mysteriously pulled away into another hatch in the floor.

Wheatley then attempts to kill off the player, in lack of knowledge of what else he could do in the moment, but having only just been plugged into the Central Mainframe, he only knows how to unclog the neurotoxin, pull up GLaDOS' old rocket turret, and how to move unmoving crushers into the chamber. The player corrupts the core again manually, and the Announcer, in a glitched procedure due to current circumstances, pulls Wheatley out without having a replacement core ready. The player then takes a lift that suddenly appears out of one of the hatches in the floor, and meets GLaDOS in the maintenance areas underneath the Central AI Chamber.

GLaDOS is still alive and active; using what limited control she had left, she moved her head out of the chamber and mounted it to a hydraulic arm, as Wheatley had done at the beginning of the main story in Portal 2. She laments to the fact that she normally would have left the player for dead with Wheatley had things not been the way they were; she knows something is happening, but thinks little of it as Wheatley is just a dumb little moron of a core. She then enlists the player to make their way through the facility from there to the nearest supplementary control room to find out what has happened.

Obtaining a portal gun and heading through some offices and test chambers, the player finds a control room with an employee's computer login information conveniently available on the desk. Logging in, they find out that the very employee whose login they were using had created a self-destruction protocol for the facility, named "Override Gamma." As the files on the computer dictate, the employee was inspired by watching too many cartoons with evil villains who used such technology in their bases. The employee ended up being fired, but before being forcefully evicted from the premises he had wired it into the Sector C power grid; the very power that Wheatley had turned on after the player left their relaxation vault.

The player then enters a nearby elevator turbine checkpoint (All of the modern elevators in Portal 2 run on the pneumatic tube system, for those unaware of that detail) and as they attempt to find out more, Override Gamma kicks into further action and removes GLaDOS from her position, far out of view of the player and only acknowledged by a shout from GLaDOS followed by a shaking and several lights going out. The player manages to use the terminal to hail an elevator into one of the turbine checkpoints, and takes it back up to the docking station where their adventure started.

Making way back into the intermediate office area where Wheatley activated the power, they find GLaDOS moved into a potato battery, where they then pick her up and use her to access a nearby testing track entry. Moving through more chambers, the facility's state worsens as the player finds a break in the chamber walls that leads to a pipe system they can take to a place where they can stop this chaos; the Override Shutdown annex. (All in all, the Override Shutdown annex is a glorified version of the Task Manager found on many computers, if not all of them.)

There the player finds Wheatley, who had also made his way there in an attempt to stop the facility from exploding. The player walks up to the console and presses a button to shutdown Override Gamma, which the terminal had been targeting since it was activated but needed manual input to take action. Before the console can fully delete Override Gamma, Wheatley blows it up in frustration that the player did not let him try to fix things, further worsening the situation.

With the console now broken, Wheatley flees in a panic in an attempt to find another way to stop the inevitable explosion, or else a place where he could potentially hide and survive it. GLaDOS, seeing the malfunctioned console, sees that there is only one solution to the problem left; plugging her back into the Central Mainframe. Now that she knows what the problem is, and now that Wheatley is no longer occupying the chassis, she can stop this. The player makes their way back to the Central AI chamber and plugs GLaDOS in, also relinquishing their portal gun in hopes that the threat is done with.

With GLaDOS newly informed of the problem and plugged back into the core, she resolves the problem in an instant and chooses to let the player leave. Before their lift departs, however, GLaDOS reveals that in the instant she resolved the problem of Override Gamma, she also had the Party Escort Bot retrieve Wheatley, and his screams are heard as the player is sent upwards to their freedom.

The lift stops in a messy office corridor, with debris strewn about from the last employees who had been here. At the end of the corridor, an exit door reveals a beautiful sunset over a wheat field outside. The player makes their escape, as Wheatley is taken to the Override Shutdown annex to have him shut down, presumably forever.

And that's the end of the story. Right? Now you know the whole tale. Have a nice day!