Luigi had recently improved to the Tick Tock Clock into a time machine. Mario comes into the adventure from a recent ride on his go-kart to the castle, joining Luigi in the journey with his new time-roving mechanism. They come to the time 2001, September 11, to fix a disaster that would scar the world for years. They prevented two planes from smashing into the World Trade Center by killing the suicidals who took over the planes under the order of Osama Bin Laden.
The brothers go to the present, where they discover that the Mushroom Kingdom is smoldering in ruins. Mario is scared and confused, as he walks through the black chambers. They notice King Bob-omb, who is extremely surprised by the arrival of Mario, claiming that he was supposed to be dead. Mario asks why, and the King says that when Mario killed two of Osama's henchmen, Osama got so enraged he destroyed Luigi and Mario and what was related to them.Mario seeks help from Professor Oak, who hands Mario Celebi, a time travelling pokemon worthy of a short-time replacement for the time machine. Mario fix the past by undoing the things they did, and the world was back to peace. Mario discovers Luigi back in the present, and discusses about their adventures. They have learned a valuable lesson... doing positive things in the past may cause danger in the future.