You wake up locked in a cell with another Wastelander. She's no happier to see you than you are to be an alien test subject, but having you around lets her devise a plan to get out. After busting out of prison, you run across a little girl with way too much knowledge about the ship (apparently the little girl is better at getting out of her cell than your cellmate) and various people frozen in cryo chambers. Together you decide to take down the ship's crew and escape.
Remember how I said Mothership Zeta was a "full circle" for Fallout 3? Similar to Operation: Anchorage, Mothership Zeta is a linear shooter, once again building on the game's weakest elements. The entire four-hour experience consists of walking through tight corridors blasting aliens and robots. If the FPS part of Fallout 3 was good, this would be a must-have experience, but it isn't.
To its credit, Mothership Zeta starts out in a really interesting place. Fresh out of your cell, you're forced to make do with whatever alien technology you can scrounge up. Beating back aliens with little more than a stun rod and uniform I was able to pilfer from a body was fun. About 10 minutes into your escape, you find all your old equipment and things go from interesting to dull. I see why you get your gear back, but couldn't it have come AFTER you complete your mission on the ship? With the type of hardware you're likely packing by now, you would think the aliens would see it as a trophy, not as something you throw in a box 10 feet away from the prison block.
Mothership Zeta also removes most instances of choice. Outside deciding to not shoot alien workers, I can't think of many tough decisions I had to make and the one choice I did make lacked the sort of payoff I would expect. Missions goals aren't very compelling either. Other than the final climactic (but lackluster) battle on the bridge of the ship, all you're really doing is blowing up power generators. Basically, its everything you would expect from "Generic Sci-Fi Shooter 3" and not Fallout 3.
