Chapter 1:

https://pastebin.com/GNWEE3iv

The Combine find the Borealis, but the Resistance has been carefully watching Combine, and the discovery the Borealis plays right into their hands to destroy it.

Chapter 2:

https://pastebin.com/6bcMA6Gq

Elite Resistance fighters travel to the Borealis, hitching a ride on Combine cargo dropships. Gordon and Alyx review their attack plan.

Chapter 3:

https://pastebin.com/j1s0Ffzt

A battle begins for control of the chasm in which the Borealis has wedged itself. Gordon, Alyx, and Dog have found themselves on the wrong side of the front line, but Gordon and Alyx fight their way to fellow Resistance fighters, helped by Dog who stays hidden in the dropship container.

Chapter 4:

https://pastebin.com/x3dxSkp0

Gordon helps the Resistance overwhelm a key point in the Combine defences, and the battle becomes utterly one-sided from there. However, just as the Borealis is about to be destroyed, an unexpected last survivor of the Combine defence shows up, and causes a serious accident.

Chapter 4.5:

https://pastebin.com/c5iqVrwe

Having interfered with the plans of the Resistance by meddling with what it shouldn't, Carrier 532 continues to blunder through life, becoming a hero for a Combine industrial world.

Chapter 5:

https://pastebin.com/naxZx0gS

The Borealis is flung through the multiverse, and when it finally settles, it is high in the clouds of a small alien planet. Gordon and Alyx have several minutes to enjoy the view, before gravity slams them into the ground.

Chapter 6:

https://pastebin.com/zyg7t35K

Surviving thanks to the environment granting them a low terminal velocity, Gordon and Alyx get their bearings, and learn about the planet they've landed on. Gordon resolves to make it back to Earth, and begins repairing the teleportation equipment.

Chapter 6.5:

https://pastebin.com/GMPcFqJY

The Resistance mourns the loss of their heroes and dead comrades, bidding their farewell. However, one Resistance fighter has been left for dead; so rather than just be a casualty, they hatch a plan to guarantee the Combine will never recover the Borealis.

Chapter 7:

https://pastebin.com/01pgJApx

In search of food, Gordon finds the corpse of someone who might just save their lives from beyond the grave, thanks to a book he wrote.

Side notes:

There are some specific details about both the workings of Half Life's multiverse and programming of this game.

This script relies on those details, thus they will be explained as more chapters are written.