When Professor E. Gadd unveils a time machine at Peach's Castle, Princess Peach travels into the past and never returns, and a hostile alien species called the Shroobs comes spilling through the rift. The Shroobs have overrun the Mushroom Kingdom of the past and taken Peach captive, so Mario and Luigi venture back through time to save her. There they meet their own infant selves, Baby Mario and Baby Luigi, and the four team up, combining the abilities of the grown brothers and the babies to solve puzzles, recover the scattered shards of the shattered Cobalt Star, and drive back the Shroob invasion.