Part 1:
Anyways, After Mario and Luigi reach the mansion, the discover that it's actually quite nice. The sun is shining, the mansion looks beautiful, heck, they even were able to look over the sketchy sign that says "Mansion" nailed over a sign that says "Ghost House!" When they enter the mansion however, they discover that something isn't right about the place. Suddenly, the front door locks behind them, trapping them inside. A storm from out of the blue crackles in the background, and then...BOOS! Several boos swarm the brothers, backing Luigi into a closet, and Mario up a stairwell. Mario gets backed up stairs so far that he is eventually forced into the Attic, where a large painting of what appears to be Peach's Castle and Toad Town sits, collecting dust. Then,the lights go out. Pitch black. And that's where the real game begins.
Part 2:
Mario wakes up in his house as if what had just happened...never happened. He barely even remembers the events that occurred in the mansion. When Mario heads outside for the second time, he discovers that Luigi isn't there, but rather a Toad is there, jumping up and down. Mario determined for himself that Luigi had gone missing. Mario also knew that this Toad had something urgent to say, so Mario asks the Toad what the matter is. The Toad says (and this will completely take you by surprise) that Peach has once again been kidnapped by Bowser, and that Bowser has once again scattered the precious power stars across the world. However, something is different about that Toad. This particular Toad was acting rather...off. For one, the Toad twitched and stuttered as he spoke. He would even contradict himself, as if he wasn't even Toad at all. Alas, Mario barely notices the strange behavior in the fungal messenger and heads of to the castle to begin his quest to save Peach, and find Luigi.
Part 3:
During part three, Mario has access to easier stages that require less stars to unlock. When he has enough (and it won't be a lot of them), he will be able to unlock the door to the first of Bowser's hideouts. When he finally reaches Bowser, he too acts very strangely before initiating the battle. Mario takes more notice to the behavior, considering how strange all the other people acted through-out part 3. When Mario defeats Bowser, he obtains a key to another part of the castle. Then something you would not expect happens...you switch over to Luigi's part of the story.
Part 3.5:
You switch over to Luigi to find yourself in a dark, cramped room. The closet that Luigi was backed into earlier. When Luigi exits after building up some courage, he discovers that Mario has gone missing. Suddenly, a slightly larger ghost appears and frightens Luigi, only for the impeccable Professor E. Gadd to show up and suck up the ghost with the Poltergeist 600 (his new prototype) and save him. After whispering a strange message into is vacuum, Gadd greets Luigi, and explains that both of them have been locked in the mansion by evil boos. Luigi asks where Mario is, to which Gadd replies that he doesn't have a clue. Gadd also acts very strangely for the duration of the conversation, but Luigi barely notices. Gadd explains that the both of them need to get to the top of the mansion (which is a rather tall mansion at that) for some unexplained reason. Luigi will go through a few sections until he encounters a boss, and the door to the second floor becomes unlocked. When Luigi enters this door, the game switches back to Mario.
NOTE: Parts 3 and 3.5 will repeat about 4 more times with an increasing difficulty curve and more strange happenings and behaviors until parts 7 and 7.5.
Part 7:
After going through a stranger, longer, and definitely tougher part of the game, he finally reaches Bowser's final hideout. The strange part is that this hideout looks eerily similar to World 1-4 of Super Mario Brothers. Then the "boss" occurs. Mario, on his own, without any player input, just walks past Bowser and activates the axe at the right end of the bridge. Bowser falls, yelling "Nooo!" Bowser lands on the lava, but doesn't fall through, or even gets burned or hurt. Bowser, Mario, and even Peach, who somehow managed to escape her cage, are all confused as to why Bowser survived. Suddenly, the whole castle shakes violently, as if an earth quake was happening,but that wasn't the case. The background starts randomly changing into other default backgrounds, and blocks start either falling away, or becoming these strange flashy glitch tiles. Was the whole game coming apart at the seams? Or was something else happening? It almost seemed as if the entire Mushroom Kingdom was falling, as if something had dropped it. and then, everything goes dark, and you switch over to Luigi.
Part 7.5:
Luigi and Gadd, whom the latter was acting extremely off by this time, had finally reached the attic. Luigi notices a large painting of the Peach's Castle and Toad Town and goes to examine it. Suddenly, Gadd screams at Luigi to stop and not touch the painting. He says something that he promptly cuts himself off of from saying,in a "never mind" kind of fashion, but Luigi already knows something is up. Gadd managed to say "It's part of my master plan" before stopping himself, and it is at that point that Luigi believes that this wasn't the real E Gadd...or atleast, was the real E Gadd at the moment. When Luigi questions Gadd for the final time, Gadd attacks him. He reveals that it was actually King Boo who was in control of Gadd's body during their little adventure, and that it was all a distraction so that his plan, "Giga Ghost," could be ready in time. He also reveals that the large painting is actually a cage that he placed the entire Mushroom Kingdom inside of so that Mario and the other residents couldn't get in his way. It is then that Luigi realizes that he can only stop the evil Boo's plan by destroying that painting. The possessed Gadd attempts to attack Luigi in multiple different ways, and Luigi cannot hurt him. The only way he can defeat King Boo is if he pushes the painting out of the mansion, so that it can fall and break upon impact with the ground. Too so, Luigi must doge Gadd's (King Boo's) attacks until Gadd breaks the wall away so that Luigi can slowly push the painting out of the hole. When he finally gets it all the way through, it plummets down until it breaks, and everything goes dark again.
Part 8:
Mario, Bowser, and Peach wake up in the ruined final hideout of Bowser, and notices that a strange, tall mansion, with an even stranger purple glow emitting from the roof in the distance. Mario recognizes the mansion immediately and runs off to it. He finds Luigi and embraces him, until the possessed E. Gadd bursts through the front doors. King Boo phases himself out of Gadd's body and looks up at the roof to notice the purple glow. He says something along the lines of, "Lovely, it's ready. That whole conundrum with the painting doesn't even matter now. I have managed to distract ALL of you long enough for my plan to finally be set up. Say goodbye to everything you knew and loved, for this is MY world now. I bet you don't even know how it feels to lose someone forever, because I CERTAINLY did! You...you FIENDISH plumbers defeated my brother, don't you remember? I bet you don't even remember that poor fellow from 'Donut Secret House,' do you?" Without another word, King Boo floats up to the roof of the mansion. A few seconds after, a door with a star lock appears, and then a booming voice is heard from the roof of the mansion, "Why don't you join me and DIE?" This door requires every star in the game (which it's currently undecided as to what that value is) to enter. Because the Mushroom Kingdom is now back in it's proper place (and mostly intact), Mario, Peach, Luigi, and a Toad found back at the castle are all playable in the castle so that getting the remaining stars will be easier. Some of the stages even require you to be any character that isn't Mario. However, Mario is the only character allowed into the final door, and once he enters it, he is taken directly to the roof.
Part 9:
When Mario finally gets on the roof, it seems silent for the longest time. So long in fact that Luigi and E. Gadd were able to make it up to the roof as well. Each one is perched atop a chimney, with the two chimneys being at opposite ends of the roof. The silence ends when a GIGANTIC King Boo emerges in a similar manner to the final boss from Yoshi's Island, and even has similar music. After some dialogue, the final battle begins. Luigi acts like a blue beach koopa, pacing back and forth atop the chimney he's on and kicking objects to Mario. Gadd acts like an NPC generator and fires objects at Mario. Mario can take any of these objects and throw them above the screen, to which they'll fall back down in the distance and hurt Giga King Boo, until he has landed the final hit. When he lands he final hit, King Boo acts like he's crippled for a split moment before showing off an evil grin. He tells Mario and co. that, in fact, the entire battle was ALSO a distraction, and that the whole "Giga Ghost" operation was only part of his plan. He sarcastically says goodbye to the heros and disappears. The Mario Brothers know that their world still isn't safe, but that King Boo won't come back for a little while. It will only be a matter of time before he returns, but they can at least celebrate their temporary success with an good ol' Super Mario World styled credits scene and some cake at the castle.
And that's pretty much it for the story besides the looming fact that there is still more to come.
