Borealis

Overview
The Borealis is an Aperture Science shipping vessel that disappeared, along with part of the drydock upon which it was stationed, under mysterious circumstances. It became a legend amongst the scientific community; it was assumed, given Aperture's infamously blasé attitude towards safety and accepted scientific principles, that the Borealis contained an immensely powerful and dangerous secret.

Many years after the Combine invasion of Earth, Judith Mossman, a Resistance operative, found the Borealis in an arctic location. She was attacked by Combine forces soon after, and was only able to send an incomplete transmission of her discovery to the White Forest Resistance base. This was intercepted by the Combine, and in turn stolen back by Gordon Freeman and Alyx Vance from the Citadel Core during their flight from City 17.

Mossman was cunning enough to encrypt images of the Borealis itself within her message. Once Eli Vance and Isaac Kleiner had decoded these and realized the full significance of the transmission, a rift opened between the two Resistance leaders. Kleiner believed the technology the Borealis contained could be used by the Resistance against the Combine; Vance, haunted by memories of the Black Mesa Incident and by the message conveyed to him by his daughter, believed that the Borealis had to be destroyed at all costs.

It is not known whether the Combine know of the Borealis, and consequently if they themselves have some interest in the ship's contents. Given the attack upon Mossman's forces, the interception of her message and the fate of Eli Vance, it seems very likely.

The Borealis is expected to appear in Half-Life 2: Episode Three. A recently released concept art reveals a ship, which on it reads "B-EALIS", where the O and R are covered by combine tech, stuck in ice, but also what appears to be Citadel Tech sticking in it, and advisors floating through the canyon. It is most likely that the combine have already found the Ship and are using its "technology", this also hints a darker storyline in Episode Three.