You are now entering the derelict boneship, and these levels are much more different than those of the previous 2 stages of the game. There are numerous places where walking up to an invisible door will cause it to simply dematerialize, revealing the room behind. In addition, there are opaque "walls" and semi-translucent veils that you can simply walk through with no need for explosives to open them. While there are lots of walls that will require seismic charges or grenades (or the smartgun) to access, the detailed organic look within the boneship can make them even more difficult to spot, increasing the value of your motion tracker and map.

You will also be traversing the PILOT'S CHAMBERS (Levels 321, 322, 323, 324, and 325) a total of 5 times. There are 8 pairs of opposite-facing alcoves within the PILOT'S CHAMBERS, and you will begin and end these 5 levels through different entrance and exit alcoves each time. In each case, you will re-enter each PILOT'S CHAMBERS level at the paired alcove directly opposite the last one you exited from. The exit in each of these levels will usually be approximately halfway around the circular level from the entrance alcove, sometimes closer, but you will need to make at least 1 full circuit of each level in order to kill all of the enemies. There will usually be only 1 or 2 kinds of aliens each time you traverse these levels; the fifth level will be a hazardous and hard-to-survive exception. On all the PILOT levels there are aliens that do not materialize until your second circuit through that part of the level, and 3 levels contain powerups that do not appear until your second pass. There are also multiple sites where aliens will materialize near your location the instant you reach a certain point or touch a specific powerup. In some cases you can actually watch the enemy materialize if you look in the right direction when you touch the triggering site or powerup. On the HARD difficulty setting, you will not be able to avoid reactivating any of the expired aliens you pass unless you accurately use a grenade or seismic charge during the initial encounter. For consistency and ease of description, all the walk-throughs deal with these levels in a CLOCKWISE DIRECTION, and the 8 paired alcoves are NUMBERED FROM WHERE YOU START in each level. Tough it out, and in the end you will be rewarded with a just-too-nifty look at the space jockey itself on your final pass through these chambers.