Plot

Main Campaign
Portal:Access All Areas takes place during Half-Life 2 and Half-Life 2: Episode Two, coincidentally with the actual Portal.

Aperture Laboratories #157 is located in the middle of the Wastelands. The facility is the final stand for the Aperture Staff. Their village is barren, overrun with Zombies and Antlions. The facility itself is protected and cloaked.

The first story
The first story is based around the final scenes of Portal. The Massive Portal's output location was the designated Aperture Repair Facility. Chell is transported there, along with GLaDOS wreckage.

Being the main base, Chell was there to apply for the activity. She is healed, and allowed to go anywhere in the facility to compensate for Enrichment Center #751's fault.

Then, in the mod, you can explore the inner workings of the facility, take the new tests, or play the Survival Campaign.

The second story
As the so-called "dinosaur" updates arrived, following the announcement of Portal 2, the new story had to be thought out. It is unknown, and will probably not be made until Half-Life 2: Episode Three or Portal 2.

However, ASBusinessMagnet has attempted to help by creating the Portal 2 and Episode Three speculated storyline pages, though they were futile in finding the real story and ending, and after ASBusinessMagnet himself thought about it, they were deleted.

The pages about the finding of the new story suggest that after whatever happens to Chell in Portal 2, she's taken back from the Portal 2's time to the Episode Two's time for unknown reasons.

The third story
The third story is largely unknown. It is known that, based on the final scenes of Portal 2, you are not playing as Chell, yet the basic 'access-all-areas' concept remains.

Survival Campaign
This mode is basically a redux and addition of the mod's maps. Merging Portal and Half-Life 2, it has a strong storyline of Betrayal, Adventure, Tragedy and Combat. The campaign will take you through Aperture's endless corridors, the ruins of the wastelands, the eerie ruins of Aperture's work village and even sections of the Combine-patrolled areas.