Half-Life 2: Episode... 3?

Quote (Sora-Chan)

Just cause they are going to that ship, doesnt mean that the portal gun will be on that ship, Aperture Science was probably working on more than just the portal gun, so theres most likely more than just that for tech.

According to Aperture Science's website (Yes, they had a mock-up website for it), the only other thing Aperture Science was working on was Military-grade Shower Curtains. Given how the big-mysterious-ship did-something-possibly-plot-vital, I'd say it's highly likely that the Portal Gun, or another version of it, is on board.
Steve dont worry about the first story, hopefully later this year, like this fall, Black Mesa will get released. Its a Mod for the source engine that recreates the first game, but majorly upgraded, unlike Half Life: Source, which is merely a port.

Basically, all you need to know is that Black Mesa opens up a portal to an alternate universe, aliens pour in and then the whole world gets shot to hell.

And it's all this guys fault.

Awesome pic of the GMan.