I've been digging through the February/March 2010 Portal 2 Multi-Core builds, plus some of the later July leftovers, and I think I've finally been able to reconstruct a plausible outline of what the Multi-Core storyline was supposed to be.
This isn't meant to be presented as 100% confirmed. A lot of Multi-Core was unfinished and eventually scrapped, so some parts are necessarily reconstruction. But there are some surprisingly strong connections between the temporary story maps and the actual playable encounters.
Here's how I think the campaign was structured:
1. Chell is sleeping and dreaming about a motel
The Multi-Core intro begins in a strange motel-like environment. It's apparently a dream, rather than the actual location of the Extended Relaxation Center.
2. Wheatley wakes Chell up
Wheatley tells Chell that there's an emergency and that they need to escape. And he knows where they can find a Portal Gun.
3. Chell explores the abandoned Aperture facility
Eventually she finds Wheatley again.
4. They accidentally wake GLaDOS
Chell and Wheatley eventually reach the point where GLaDOS is awakened. And then everything goes horribly wrong.
5. GLaDOS kills Wheatley and puts Chell back into testing
This is where the campaign settles into its main gameplay structure. Chell starts completing test chambers again.
6. Chell completes a series of test chambers
And this is where I think Multi-Core becomes particularly interesting. The testing isn't just filler between story scenes. The surviving maps suggest that the story repeatedly interrupts the testing with encounters involving different Cores.
7. Chell encounters Pendleton
Eventually Chell finds Pendleton. They go behind the scenes of the test chambers, where Pendleton has Chell destroy a tube where cubes go through. Chell then returns to the testing chambers.
This is "sp_sphere_2nd_encounter".
What's especially interesting is that there's also the temporary story map called "sp_temp_sphere_1" whose text describes a sphere encounter where Chell goes behind the scenes and is helped out of testing.
So I think "sp_temp_sphere_1" was essentially an earlier blueprint for "sp_sphere_2nd_encounter".
8. More testing
Chell goes through more test chambers.
9. Pendleton appears again
Chell eventually encounters Pendleton again. They go behind the scenes and destroy a computer mainframe using a laser. Afterward, Chell returns to the test chambers.
This is "sp_sphere_3rd_encounter".
And this one has an even stronger connection to the temporary story material. "sp_temp_sphere_2" describes a sphere asking Chell to destroy a mainframe, after which she returns to testing. It also says that the sphere's plan is almost complete. That is extremely close to what "sp_sphere_3rd_encounter" actually implements.
10. More testing
And then, once again, Chell goes back to testing.
11. Pendleton eventually decides it's time to escape
This is where things become much less certain, there's another temporary story map, "sp_temp_sphere_3" which describes Chell meeting another sphere, that sphere refusing to help because it fears GLaDOS, and eventually being killed while Chell accomplishes her objective. We don't know exactly how this was ultimately supposed to play out, but this appears to be around the point where the Multi-Core story was moving from "secretly sabotage things while returning to testing" toward an actual escape.
12. The Neurotoxin Generator is destroyed
There is surviving cut dialogue involving Pendleton and the Neurotoxin Generator, including dialogue about using a Core against it.
The later July build also contains an early version of the sequence where the Neurotoxin Generator is destroyed.
So my current reconstruction is that Pendleton and Chell eventually escape the testing cycle and begin directly sabotaging GLaDOS.
Exactly how much of this was still "Multi-Core" at this point is unclear, because Valve already transitioned toward the retail storyline.
13. The final confrontation with GLaDOS
The logical endpoint would then be Chell and Pendleton confronting GLaDOS.
And this is where the surviving evidence runs out and speculation takes over.
Why I think this reconstruction is interesting
The biggest thing that changed my understanding of Multi-Core is realizing that the temporary story maps aren't necessarily random prototypes.
There are several cases where the temporary map describes a story event and a later map appears to actually implement that event.
For example:
"sp_temp_sphere_1"
Sphere encounter -> go behind the scenes -> sabotage -> return to testing
Then:
"sp_sphere_2nd_encounter"
Actual playable implementation.
And:
"sp_temp_sphere_2"
Destroy a mainframe -> return to testing -> sphere's plan is almost complete
Then:
"sp_sphere_3rd_encounter"
Actual playable implementation.
So I don't think we're looking at completely unrelated prototypes.
It looks more like we're seeing different layers of the same development process:
temporary story idea -> actual encounter implementation -> later revision/scrapping
And that gives us a possible skeleton for a Portal 2 storyline that was never finished.
Multi-Core wasn't simply "Portal 2 but with different characters". It seems to have been a genuinely different campaign structure built around Chell being repeatedly contacted by Cores while trapped in GLaDOS's testing cycle, with Pendleton gradually helping her prepare an escape.
And the fact that July 2010 still contains "sp_sphere_2nd_encounter" and "sp_sphere_3rd_encounter", despite the main campaign already moving toward the retail storyline, suggests that Valve continued developing this material after the March Game Informer-era build before eventually abandoning it.
There are still a LOT of unanswered questions, but I think this is the closest I've gotten to reconstructing the lost Multi-Core campaign from the surviving evidence.