The Incredible Machine's creation is largely due to the genius of Isaac, who ceases his work on it when he realizes what Team Dim Sun plans to do with it. However, the Sinis Trio kidnaps Isaac's sister and forces him to complete it on threat of hurting her. The player and Keith then go to Altru Tower to rescue Isaac before he can complete the machine. Unfortunately, the machine is activated just before they reach him.
The Incredible Machine is at first shown to have three levels, named simply Level 1, Level 2, and Level 3. As the player and Isaac race to the top of the tower, disabling its three barriers, the machine's power gradually increases with each passing level. Upon disabling all three barriers and reaching the top of the tower, Blake Hall is already there. At this point, Hall reveals that the Machine in fact has a fourth level, named Level Dark, which he calls the "forbidden level". Despite Wheeler reminding Hall that he said himself that it is impossible to know what kind of consequences such a level could have, Hall powers up the machine to Level Dark anyway and attacks the player with Darkrai, who is under his temporary control.
In a special mission, Liberate The Tower!, Team Dim Sun's remnants form into Team Debonairs, led by Kincaid. They take control of the upper floors of the Altru Tower, and try to turn the Luminous Crystal back into the Shadow Crystal by removing the Tears of Princes. The player needs to capture Kincaid's Drapion and Gliscor with Darkrai's help to complete the mission.