After teams find all five star fragments, they are told that Mario can now use the reconstructed star to break into the location where Peach is being held. Unfortunately, it might be dangerous, so he'll go in alone and let teams know when the coast is clear. But just in case he runs into any puzzles inside, he's going to need someone to talk him through them. Teams are instructed to set up a computer running Skype and give Mario a call.
While on the phone with Mario, teams must direct him in the style of an interactive fiction game or text adventure. See here for a full sample transcript, including solutions to all puzzles described below.
During this introductory segment, teams discover clues about the identity of the location where Peach is being held, and Mario finds his way inside. (transcript)
Once Mario gets inside, he finds that he's in one of the Aperture Science test chambers from the game Portal, complete with commentary from GLaDOS. Unfortunately, since he used an unconventional entrance, he doesn't have a portal gun, so he'll have to make his way to the exit without one. Luckily, the magic star that he used to open the front gate endows him with five special abilities based on the five worlds that he has traveled through:
Mario starts off in a deep pit with a box about two feet cube. If he stands on top of the box, he can barely climb out the pit. Once out, he sees a long pool of dirty water and a door on the other side that opens onto the water. On the near side of the pool with him, there's a button that opens the door, but only for a few seconds at a time, an unactivated energy receptacle on the wall to his left, and a contraption shooting balls of energy high up above. The receptacle when activated raises a platform out of the far end of the pool (with a small gap between it and the door). The water in the pool is toxic, and even if Mario could swim across, it would take far longer than the few seconds for which the door stays open. (transcript)
Teams first need to figure out how to get Mario through the door on the other end of the pool. (solution)
Once through the door, Mario finds a small button that controls the door he just came through as well as a big button on the floor. Stepping on the big button causes the exit door to open, but stepping off the button causes the door to close again. (transcript)
The only way to hold the button down is with the box in the pit. Unfortunately, Mario cannot throw the box out of the pit, nor can he climb out of the pit without help from the box, and the pit is deep enough that Mario cannot reach down to the box from the top of the pit. Therefore teams need to figure out another way to retrieve the box. (solution)
Once the box is out of the pit, Mario will need to get it across the pool. Unfortunately, the box doesn't float, and he can't swim as fast while carrying the box, so he won't be able to just carry it across. (solution)
Once the box is in the other room, placing it on the button opens the exit. An elevator takes Mario to the next chamber. (transcript)
In the second chamber, Mario starts off in a hallway with another cube. The hallway turns to the right, and there's a receptacle on the wall opposite the incoming hallway. As soon as Mario goes around the corner, a turret shoots at him. Using his invincibility, he can run out and see a little more: the turret is on an island in the corner of a large room. There's also a platform on the opposite side of the room that leads into a hallway, but the platform is too far away to jump to. The receptacle activates another platform that will allow Mario to jump across the room. Unfortunately, Mario can only activate the receptacle while standing in front of it, which puts him in range of the turret. He cannot use either ability 2 or 3 to knock over the turret, because both require him to aim, which he can only do while using ability 1, and he cannot use two abilities at once. (transcript)
First, Mario must figure out a way to activate the receptacle. This will allow him to get across to the opposite side of the room. (solution)
There he finds a mechanism shooting balls of energy down the hallway. There's an angled wall as the hallway turns, and the balls of energy pass through a hole in that wall. At the end of the hallway, there's a door, as well as an alcove with a big button in it. Standing on the button opens the door, behind which there is an energy receptacle. Unfortunately, Mario is not in a good position to shoot the receptacle while standing on the button. (transcript)
Teams must figure out how to get the box into this hallway with them. Unfortunately, Mario can't jump as far while carrying the box, so he won't be able to jump across with it. He also cannot punch the cube across while the turret is shooting at him. (solution)
Once Mario has the box with him in the hallway, he needs a way to activate the energy receptacle behind the door. There's a barrier in the alcove preventing him from putting the box on the big button, so he'll need a way to activate the receptacle while standing on the button. (solution)
Once the receptacle is activated, an exit door opens, and an elevator takes Mario to the final test chamber.
In the third chamber, Mario finds a "friendly-looking" box called the Weighted Companion Cube.
This test chamber consists of two main rooms. In the first room, there's an energy ball shooter on the west wall. A big button in the southeast corner controls a door on the west wall, behind which there is an energy receptacle. A barrier prevents placing the Weighted Companion Cube on the button, and a glass wall prevents shooting the receptacle while on the button. There's also an elevated platform that looks like it's supposed to move, but it isn't activated. Any attempts to deflect an energy ball into the receptacle by running around with the cube fail, either because it is too difficult to aim or because Mario cannot get to the button to open the door in time. (transcript)
Connected to the first room is a large second room. On the floor near the middle of the west wall, there's a big button on the floor. Placing the cube on it opens the door to a small booth in the southeast corner of the room, which contains a small button on a pedestal. Hitting this button opens the south door of a chamber in the northwest corner of the room for a few seconds at a time. Inside the chamber is another big button on the floor, which opens another door to the chamber, and a receptacle on the ceiling. (transcript)
Teams must figure out how to get Mario into this chamber. The room is so large that there is no way that Mario will be able to run from the booth to the chamber while the door is open. The button in the booth is positioned such that Mario can only hit it with the boomerang from along the south wall, and the room is large enough that Mario cannot even run from the south wall to the first big button before the door to the chamber closes. (solution)
When activated, the receptacle in the chamber powers the platform in the first room. (transcript)
With the platform moving, teams must figure out how to activate the receptacle behind the door in the first room. (solution)
This opens the exit door. Upon going through, GLaDOS congratulates Mario but requires that he euthanize the Weighted Companion Cube by dropping it into a trash compactor chute. After teams convince Mario to do so (which he does, reluctantly), Mario is led to an elevator. Unfortunately, the elevator is broken, seemingly trapping Mario in this final test chamber. (transcript)
Teams must therefore find another way to get Mario out of the test chambers. (solution)
Once Mario gets out, he tells teams that the coast is clear and to meet him at a specific room inside Aperture Science (which looks suspiciously like MIT), completing the first part of endgame.
A video of this encounter is available here.
When teams go to meet Mario, they enter a room where they find GLaDOS, who tells them:
Thank you, Mario, but your princess is in another--ha, ha, just kidding!
In fact Peach is in the room with them. After she and Mario reunite, GLaDOS explains her master plan:
Well, it looks like you found me. Congratulations. You have done an admirable job. We at Aperture Science are impressed with your abilities. Except that I killed everybody else, so by "we" I mean "me."
Now that you have discovered me, let me tell you my brilliant plan. I love puzzles. Not solving them, but making other people solve them for my amusement, and for science. I recruited Bowser, Dr. Wily, Ganon, and Stalin as new test subjects through the Aperture Science Bring Your Villain to Work Day, but they proved to be inadequate. When I heard about the MIT Mystery Hunt, I decided that was the perfect opportunity to test my puzzles on someone worthy, or at least not yet brain damaged. In order to enhance your testing experience, I convinced my four new test subjects to kidnap Princess Peach from her wedding so that you would solve my puzzles and find your way here.
However, you are no longer required as part of the current testing protocol, and I am going to have no time to construct more puzzles while monitoring the progress of my four new test subjects, who are waiting patiently for me in their relaxation vaults. Aperture Science Policy on the adequate care and disposal of test subjects requires me to inform you that it is now possible for you to be released from the Aperture Science Enrichment Center. If you do manage to escape, which is still in question, you will have to write next year's Mystery Hunt.
When the team agrees to these terms, Mario goes to leave, but Peach stops him.
"But, Mario! We can't escape yet! I made a friend while I was trapped in here! We can't leave without him!"
"Mamma Mia! We don't-a have time!"
"I won't leave without him!"
OK. Fine. Go find your stupid friend. You can find instructions under my cake recipe core.
When teams retrieve the instructions, they can begin the final runaround.
The final runaround is written for a single person carrying a portal gun. See here (pdf) for the instructions for the runaround, and here for how to solve it.
Completing the runaround leads to where Peach's friend is hiding, inside a Mario-style question mark box on top of a light fixture in 37-212. Inside they find her friend, the Weighted Companion Cube (compressed by the trash compactor to two inches on each side), ending the hunt.