Professor E. Gadd completed his time machine using the Cobalt Star as the energy source. The time machine was unveiled in Princess Peach's castle. Princess Peach and the two Toads entered the time machine to visit the Mushroom Kingdom's past. However, Peach's ward, Toadsworth worried about her. While in the past, the Shroobs, Princess Shroob and Elder Princess Shroob invaded the Mushroom Kingdom attacked Peach and the two Toads. Peach broke the Cobalt Star and trapped Elder Princess Shroob.
Toadsworth was worried sick for Princess Peach despite E. Gadd reassuring him that "there's a 99.999999999% that [Peach] will return". Mario grabbed the Refreshroom from Toadsworth's room and revived him. After the time machine returned, a Junior Shrooboid appeared from it. Mario defeated the Junior Shrooboid and the Toad checked in the time machine, realizing there was no sign of Peach. E Gadd stated to Toad that the Junior Shrooboid did not eat her. Professor E Gadd's DS time radar senses Peach is "somewhere in the Mushroom Kingdom of yesteryear".