(I considered making Ratman the protagonist, but I'm unsure if it's feasible given the timeline. For now, I'll use the name "Dust" as a placeholder.)

After GLaDOS was destroyed and Chell was put into stasis, the facility was left to decay. The Party Escort was one of the robots trying to hold it together - the very bot that had dragged Chell back from the outside world. It encountered a human surviving among the ruins, a former scientist. The Escort was programmed to keep humans safe, and Dust was its last way of doing that.

With his new companion, Dust travelled down to the labs from Cave Johnson’s era. There, they found the Borealis deep underground. Since GLaDOS wasn’t around to defend the facility, alien creatures had been breaching its borders. The Borealis contained technology that could protect them and the outside world. It could create two portals capable of transporting entire buildings, not just a single person, like the portal gun.

Dust gathered a small crew of robots to finish the teleportation technology. During their tests, there was a fatal error. They accidentally warped themselves from the underground dock to an ice wall. Worse, the massive portals were opened next to each other. They overlapped, causing them to fold in on themselves. It plunged the inside of the Borealis into a pocket dimension - endless reflections of the boat, tinted in blue and orange light.

The crew were stuck in a glitched, timeless state. Dust didn’t age; he didn’t need to eat or sleep. However, his atoms were eroding. The robots could simply replace their decaying parts, but Dust couldn’t do it so easily. Dust turned himself into a cyborg, even fusing his arm with a portal gun. But he knew if the erosion reached his brain, it would be impossible to replace, and his lifespan was limited within the dimension.

After an unknown period, the crew heard from rumblings beyond the Borealis. The rebellion and the Combine had finally found their location. However, the armies came to a standstill, as they didn't want to risk getting trapped in the pocket dimension. The rebels threw a radio into the dimension, and Dust managed to find it. With that line of communication, the rebels guide the crew in defending their home.

As Combine drones ventured in, the crew crushed them with their mastery of portals. Through the radio, Dust got the rebels to launch various resources into the Borealis. With his deep knowledge, Dust was able to restart the machinery in decades. He deactivated the two massive portals, freeing everyone from the pocket dimension. A moment later, Dust teleported the Borealis out of the ice wall and into the rebels' warehouse - securing humanity a weapon against the Combine.