The story goes after the events of Chaos Sky and The Hallway Cave. After the adventures they had, Mario and Luigi asked by Professor E. Gadd to help him on the research. Mario and Luigi decided to go to E. Gadd's House. Turns out, E. Gadd is not home. He's going to Icetrow City because his packages isn't send to his house yet. So, E. Gadd is going to the deliveryman to give him the packages. Mario and Luigi after reading the note. They are going to the house by the pipe to his underground floor. Looks like the underground floor is haunted and filled with enemies. They decided to clear every enemies in the mansion that Bowser's minion leader, Boom Boom set for Mario and Luigi. After switching and setting the mansion a bit, they finally found their way to Boom Boom. And confronting Boom Boom. E. Gadd finally home and asked Mario and Luigi to do the research with him about Groudon activites for the last weeks.Groudon is still asleep. E. Gadd told Mario and Luigi to rest for the night.
And just as Mario and Luigi leaving in the morning, Toad came and saying that another koopaling is going to awaken Groudon. So, away they go and confront the Koopaling! (maybe)