I didn't think about Black Mesa stealing it, I thought about maybe the Combine attempting to steal it and accidentally moving it to the wrong place. Or Rattman is confused.
So, the Borealis, an Aperture Science research vessel built WAY underground in a dry dock within the Aperture facilities during the 70's, is now somewhere in the Arctic. The transmission Mossman sent was decrypted in HL2:EP2 and it showed the actual Borealis. Now, I know that Aperture did portal...
Portal 2 came out on PS3 and it was actually fully the Source engine running on PS3, unlike The Orange Box on PS3. I'm really excited for future Valve titles coming out on PS3! I already tried CS:GO on PS3 because of the PS Plus timed trial thingy. It's nice!
On the timeline of Half Life and Portal universe it says the project got approved in 1981(the Portal project), and you can find the Borealis dry dock in the 1970's section of the Portal 2 game, so I assume they already knew what they were aiming to do with the ship, but I think they built it...