Portal will ship with Half 2 : Epidode 2, and as the title of the game suggests, the portals refer to dimensions in space that transport you to different areas of the ship. If you view the trailer you'll see that the portal gun can blast through walls creating openings that you can then jump through.
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Tip: You'll need to know a bit of DOS. Type : login, then type anything for Username and then portal for password. You can then look through the directory and try and work out what to do next.