|Spoiler warning: this article may contain major plot or ending details.|
The Incredible Machine's creation is largely due to the genius of Issac, who ceases his work on it when he realizes what Team Dim Sun plans to do with it. However, the Sinis Trio kidnaps Issac's sister and forces him to complete it on threat of hurting her. The player and Keith then go to Altru Tower to rescue Issac before he can complete the machine. Unfortunately, the machine is activated just before they reach him.
The Incredible Machine has four levels: level 1, level 2, level 3, and level Dark. As the player and Issac race to the top of the tower, disabling its three barriers, the machine's power gradually increases with each passing level. Upon disabling the barriers and reaching the top of the tower, Blake Hall is already there. Against Wheeler's recommendation, he takes the machine to level Dark 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.