I have to disagree with the status quo.
Stalkers are made by the combine from female insurrectionists. They are an inner-city phenomenon, fit for little more than simple, repetitive operating tasks. Stalkers have no relation to the Aperture Science Borealis, and I doubt they’d be useful enough for the Combine to take them along to the South Pole.
Whatever happened to the Borealis will have most likely caused most of its crew to die. The enemies left on the ship, I expect, will be robotic sentries of several types.
First, imagine the Borealis to be of a darkened, maze-like quality. Its power has worn out, or it has turned its power off to preserve energy. Much of the space inside is filled with containers and heavy machinery. The areas contain sensors that passively scan for life, and will activate the ship’s machinery in one way or another. If you are not a crew member, the machinery that will activate will be of the violent, lethal variety.
In this scenario, I expect the 3rd HL2 episode to have sneaking as its key gameplay mechanic.
1. Scout Robot
Behaves like the houndeye when it’s alone and approached. Runs to get help.
Lightly armed, maybe shoots from the shadows. Highly sensitive.
Looks like a miniature Hunter.
2. Sentry Robot
Heavier in appearance. Looks somewhat like a Star Wars battle droid, except with the white matte Aperture Science textures.
Inactive, activated when warned by a scout, or when room sensors detect life.
3. Stationary turret (Link)
We’ve seen these in Portal.