This quest starts out with your character getting probed, and you will need to mash the designated button to destroy both of them they try to use. With the second one destroyed, you gain the ability to use the alien probe to teleport using the probes around the area (and around town when you get the chance).
It should be noted that the normal aliens are especially annoying to fight, since they have a habit of shielding themselves with Refractor Shield, giving them 3 armor. They can also heal themselves for around 50ish health. This is especially troublesome since you're alone in combat.
Another thing to note is that you definitely need to explore every nook and cranny of this ship, since you will not be able to return to it after completing the quest.
There isn't anything you can do in the room with Randy Marsh, so exit via the door on the south end of the room. You'll be trapped between two barriers, with some aliens and a probe on the right side. You can shoot down the wires hanging above to take out one or two of the aliens, then teleport and take out the rest of the aliens.
To the right of the aliens should be an elevator, which requires you to use your probe on the panel before it works. In the next area, you can teleport to a middle platform with two interactive panels, which control the platforms above and below your position.
The above platform needs to be to the left in order to teleport to the top, where you'll find more aliens. Access the panel in between to shut down the force field to the left (the right has a panel that leads to a chest), where you'll have to play a Simon Says-type mini-game to try and free Randy.
Go back down to the central platform again and move the lower one to the left. Teleport to it and then inside of the tube, where you'll find some aliens (you can use environmental hazards to get rid of both of them if needed). Go to the right (check the audio log for a code), then access the panel to do the same mini-game as before, which extends a bridge near the elevator.
Back at the elevator, you can take out the other two aliens via environmental hazards, leaving you to battle alone against the Alien Chief of Security. If you listened to Randy, you have an electric add-on for your weapons, which it is weak against. Its strongest attack is Space Rage, which does a lot of hits and can cause Bleeding.
You shouldn't have too much trouble if the Chief is alone, but things can get hairy if you have the other two aliens there. After winning the battle, use the panel on the left to deactivate the force field, then go back to the room with Randy. Complete the mini-game to finally set him free and pick up the crystal that drops from the probe machine.
If you go down the ladder right outside, you can find an Alien Conspiracy Hobo hiding on the right side (optional fight, but drops equipment). At the left side of the area is another elevator, but you need to place the crystal you just got in it to make it function. The only thing really up here is a Chinpokomon sitting atop one of the monitors, so make sure you grab it. Go through the next doors to get into a boss fight.
|BOSS FIGHT: Alien Pilot|
You have to fight the Pilot, Co-Pilot, and the Defense Security Matrix. The Matrix will buff the other two and doesn't have much HP, so you should definitely take it out first, using electric attacks if you have the add-on.
The battle is still challenging, since the Pilot and Co-Pilot can fire their phasers at you, hitting you multiple times and the Pilot can call in a Photon Torpedo, which does big damage and can inflict Burning. Note that the Pilot can also raise his attack, which adds Burning to his normal attacks.
Once you win the battle, a cutscene will occur and when it's over, you'll wake up in your bed and the quest will be complete. Go downstairs and watch the news, then attempt to leave your house. Cartman stops you and says you need to recruit some more factions to help against the Elves, starting your next quest.