This quest starts immediately after the scene. Press Q to cycle with your options until the Alien Probe is selected. Now press F and aim for the alien device with an eye and click it to beam yourself to it. Now you can select the spot where you'll beam out from. Use this to escape the barrier around you.
Operate the panel to the right to reveal a glass window. Beam yourself inside the enclosure with the chest so you can loot its contents. Beam yourself out of the enclosure then go to the left where you'll find another chest. Loot it then leave the room. Before fighting off some aliens, you must equip some Shock patches to your weapon(s) since they're weak against it. You can also shoot the floating probes and the orange octagons on the walls to get some additional junk you can sell.
The aliens will erect barriers on both sides. You can enter the next room to get some items from the chest if you want. Shoot the large dangling cable to blast off some of the aliens. Once done, use the probe to beam yourself past the barrier. Use the probe again on the blue panel on the door to deactivate it. Take the elevator to the control room.
Loot the chest to your immediate left then beam yourself to the platform to the right. There are two panels here. The panel to the left controls the floating platform above while the one to the right controls the platform below. Beam down to the lower platform and use the alien probe to operate the blue button, which will open the trapdoor on the floor, killing one alien.
Return to the middle platform and operate the panel to the right to move the platform to the left. Beam to that platform and you'll be able to beam to the lower platform under the tube. Operate the panel there to activate the ventilation fan to the left to slice and dice the unsuspecting alien.
Beam yourself to the tube this time and head all the way to the right. Use your probe to shoot the blue panel past the barrier to remove it and for you to loot the chest. There's also a ledge overhead that contains an audio log and some items. After getting them, operate the panel. You have to press the same button combinations twice and another path will be opened in the left side of the room.
Backtrack again and beam up to the middle platform then operate the panel to move the floating platform to the right. Beam yourself there and loot the chest.
Return to the main platform and operate the panel on the left to move the floating platform. Beam up, use probe on the blue panel to the left to reveal an item chest. Head to the right, use Cup-a-Spell on the flaming orb to blast the nearby alien.
Take out the other alien then go past the orb. Head to the far right and push the blinking button. You can now beam to the enclosed room below that has a chest. Loot it them backtrack to the panel where you blew up the alien before. Operate it to remove the barrier to the far left.
Go in there and operate the panel. You have to follow the same color-coded button presses. However, you'll encounter very complex codes twice. Don't worry since you'll get a very simple code finally. Use that to remove the barrier in the main room next to the elevator.
There's a broken screen that you can shoot off with your ranged weapon. Use this to take out the alien below it. Once done, engage the enemies. The alien guard is a tough bastard and can inflict bleeding. Don't try to remove that debuff and focus on healing yourself instead. After taking them out, operate the panel and return to the holding area.
Before regrouping with Randy, head to the far left and loot the chest there. There's also a room to the far left that requires a White Power Crystal. There's also a ladder leading to an enclosed room below the holding area. Strike at the pile of trash there to battle a hobo. This hobo is a tough nut so you'll have to rely on Burning Damage and perfect blocks to take him out. The Tinfoil Hat you can get from him will be very useful in your next battle.
Return back to Randy and operate the panel to free him. Once done, he'll added as your friend. Retrieve the white power crystal then leave the room. Head to the left this time and place the crystal. Use the probe in your butt to activate the blue panel and call the elevator.
Ride the elevator and knock off the chinpokomon on one of the monitor screens to the right. There's also a chest that you can loot. Prepare your best gears and weapons at this point then save your game. Enter the cockpit to fight the alien pilots.
The defense matrix behind them will constantly supply them with various buffs so its imperative that you destroy it first. After the matrix is down, you can just pummel the pilots with ease. Heal yourself as necessary.
After the scenes, you'll wake up in your room and the quest will be complete. Go downstairs and watch the TV if you want. Attempt to leave the house and Cartman will barge in and give you another quest.