In the 1992 GIJOE Konami arcade game, the last stage is set aboard the "Missile Battle Ship".

I've search for a while now, and can not find any other references to this vehicle. Is this a vehicle/base that only appeared in the arcade game? Was there ever another reference in the toys/comics/shows/etc. ?

The ship is pictured below:

http://gijoe.locehilios.com/joearcade.gif

that kind of reminds me of the flying thing from the opening credits to the cartoon.

that kind of reminds me of the flying thing from the opening credits to the cartoon.

Agreed... and it also reminds me of the heli-carrier from the first mini-series. However, I can say that I have not seen this in the original Marvel comics series (however, there are a scant few later issues I have not yet read, and a number of Special Missions I have not yet read). The vehicle definitely looks very 'Cobra' - or very 'Robotech' - or very 'Shield'