My Crazy Theory (Spoilers)

[kepano]

What if all the scientists at Aperture Science escaped through a portal to the arctic where they remain in the Borealis, far from the Combine.

There they continue work on an uber portal gun and a gateway to the Combine world which they hope can be used together to destroy them for good. Of course the research is kept a secret from both Combine and the rest of humanity, fearing that their work may be destroyed by both parties (for different reasons). Aperture also fears that if the rest of humanity discovers their plan, the Combine will be one step closer to discovering their operations.

Eli's comment warning you against another Black Mesa becomes evidently clear. You arrive at the Borealis in Episode 3 where the portal gun makes an appearance and a dumbed down GLaDOS greets you (obviously she's lost her sense of irony in the downgrade). The combine begin to figure out Aperture's plan, and you have no choice but to temporarily take the portal gun into the Combine world to kick some ass.

Finally, Chell, Alyx and Mossman mud-wrestle to have your babies.

 

[Nitre]

Nah, the idea of going to a combine world isn't great methinks.

 

[kepano]

Nah, the idea of going to a combine world isn't great methinks.

Well that part is optional... It seems like it might eventually happen though, even if it isn't in Ep3.

 

[Ennui]

Earth is a Combine world.

 

[Kaepora]

Finally, Chell, Alyx and Mossman mud-wrestle to have your babies.

This should be Episode 3's main premise.

 

[kepano]

Earth is a Combine world.

I suppose that's true. I was insinuating their home world, but perhaps Aperture will merely open the gates to another planet that the Combine have overtaken, releasing yet another planet's local resistance on Earth.