The Alien Ship is the craft in which the Entity came to Earth. Warning: once you enter this level, you cannot return to the previous level, unless you turn back immediately; a situation unique in Strife levels. Although by this late stage, there's no earthly reason to turn back anyway. This ship is probably the "comet" that caused so much havoc. The décor (especially the color scheme) will look very familiar to those who have beaten Episode 1 of Duke Nukem 3D (which came out a year earlier), although of course the textures are different. SPOILER WARNING: Plot details follow.