The story takes place in the pre-GLaDOS era of Aperture Science, before she was plugged in. At this time, test subjects are monitored by real Aperture Science employees, whose work was tedious, lengthy and repetitive. This is why they decided to build a great artificial intelligence that could both replace them in these difficult tasks, and also take responsibility for many other tasks within the complex and compete with Black Mesa's superiority. All employees of the Aperture Science complex are now eagerly awaiting GLaDOS. Maybe even a little too eagerly, as the upcoming events will tell.
It all starts with a test subject (named Abby) going through the nineteen test chambers, which are considerably harder and more lethal then the ones of the original Portal (for example, turrets are encountered in the second chamber, whereas in the original Portal they don't appear until the sixteenth). After completing the test chambers, she is congratulated by the staff as being the first test subject to perform such a feat, and that a party will be held in her honour. But, GLaDOS is also being activated at the same time (even though her morality core isn't prepared yet), so, as a special treat, they invite Abby to go and watch from a secret platform.
However, soon after awakening, GLaDOS proceeds to kill all the people in the chamber, and attempts to kill Abby too, with a mixture of telekinesis and death rays. However, the remaining survivors manage to shut off the generators. Knowing they have only a little while before the emergency generators kick in, they tell Abby to get the morality core and install it before she kills everyone. After navigating through the now-destroyed Aperture Science facility, she finds the morality core and manages to attach it to GLaDOS, just as she begins flooding the place with a neurotoxin.
Abby then blacks out, and, when she awakens, is seen being dragged out of the chamber by a female Aperture Science employee. The screen then fades, and the final cutscene is that of Abby walking through the parking lot of Aperture Science (where it is now raining), collapsing, and (presumably) dying, as the screen fades to black. The last thing she can see is the G-Man, standing in the booth and adjusting his tie.
The difficulty of Portal: Prelude's test chambers is significantly higher than Portal's. The players must dodge turrets, redirect energy pellets, and avoid numerous traps. The player also manages to set the fifteenth test chamber on fire. In the eighteenth test chamber, the player must stand on buttons at the right times to obtain a companion cube, which is used to press down a button to get to the exit. The puzzle can be bypassed by firing a portal to the elevator while standing on the button. However, the player is allowed to take the companion cube with them, and they must for the next test chamber. If the player does not bring the companion cube with them, they can go back to the eighteenth test chamber through a behind-the-scenes area.
There are three observers in Portal: Prelude.
Mike is the first observer you hear. He is reading a script, when he is interrupted by Erik. Mike always seems to follow test procedure, but is kind and will spare a player if they are about to die, as seen in Test Chamber Six. (However, the effect is the same as dying, as Mike informs the player that they cannot be given a second chance.) Mike leaves for the fourteenth test chamber after it catches fire while the player is at the end of Test chamber 16. He is not seen again until the end of the game. He is killed by a rocket turret while helping Abby escape GLaDOS.
Erik is the second observer, who interrupts Mike as he is talking. Erik tells Mike to "stop this crap please" after Mike reads his script, and also tells Mike to stop calling Abby a "specimen". Erik seems kind at the beginning, but as evidenced in Test Chambers Six, Seven, and Eight, wants to kill Abby. Erik leaves in Test Chamber Four for unknown reasons, comes back in Test Chamber Seven, and leaves again in Test Chamber Nine because "this is starting to get really boring". Erik returns in Test Chamber Seventeen. Erik is killed by GLaDOS after she is plugged in.
Peter is introduced as a replacement to Erik in Test Chamber Twelve. He introduces himself saying, "I've worked here for eighteen years, and I'm not happy to be here". He is not content with Aperture Science and makes that clear to the player. However, he is kind, and saves the player after they catch Test Chamber Fifteen on fire. He also writes a shell script to replace them after they are called to a meeting in Test Chamber Eighteen. He is killed by GLaDOS when she is plugged in.
Portal: Prelude is rich in Easter eggs. Here are the ones in the current version (1.1.5 at time of writing):
- The player is able to crawl through a gap in the metal of Test Chamber Nine after reaching the other side of the glass and goo pit. After reaching the other side of the white area, the player is in a Mario-like area. After a short drop, the player can see three numbered pipes, with "Welcome to Warp Zone" written above them. If the player goes into a pipe, they can skip to another level.
- The player can either portal stand or noclip to an area below the disintegrator in Test Chamber Nine. There are cans, a makeshift bed, and "HELP" written on the wall. Upon reaching that area, Erik says, "Hey, you thought I was not watching you? Where the heck are you? I can't see you on any cameras. How are we going to get you out of here?"
- In Test Chamber Ten, the G-Man can be seen in an observation room.
- In Test Chambers Eleven and Twelve, the player can noclip to a green square outside of the map. The "Badger Song" plays, accompanied by a mass of dancing badgers.
- In Test Chamber Twelve, the G-Man can be seen through the window in the last part of the level. He disappears after going out of sight.
- When Upgrading the ASHPD in the small room you left it, having finished the test, the G-Man can be seen through the window, passing by.