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It's SUPPOSED to be on a shelf in the closet at the end of the Waste Disposal area, but there's currently a glitch where half the time it won't show up there. I've gone through Mothership Zeta twice now and it hasn't been there both times.
The sword is towards the end of the garbage area when you meet up with Sally, and right before going through the teleporter. Or if you miss the sword like I did, you can shoot it out of the samurai's hand while in the bridge.