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Mario & Luigi: Twenty Years Later is a game for Wii and Nintendo GameCube. It is set twenty years after Super Paper Mario. In the game's basic plot, Bowser has taken over Mushroom Kingdom and the Mario Bros. are nowhere in sight. Reality is also mysteriously coming apart...
Prologue, pt 1
The chapter opens in the present. The Super Mario Bros. are building a time machine, when Yoshi, excited about it, falls in. He is then taken twenty years forward in time. Reality itself seems to tear as this happens.
Prologue, pt 2
The chapter opens ten years into the future (ten years after Yoshi was sucked through time, but ten years before he would appear) as a 3-D Dimentio, having used absorbed the void, wrecks Mushroom Kingdom. Mario and Luigi try to stop it, but are battered and hurt. Finally, after a long battle, the bros. beat Dimentio and accidentally kill him. After this terrible shock, Peach decides that she wants nothing to do with Mario if he would kill someone. The bros. retire from hero work. Reality tears again.
The chapter opens ten more years later as Yoshi emerges from the time machine. He explores the city and finds out that the Mario Bros. are living in an apartment in Delfino Plaza, which has become horribly polluted. Yoshi goes there and finds that Mario and Luigi are now very old, and long since thought Yoshi dead. They are glad to see each other, but then Mario tells him about all that has happened: Bowser now owns Mushroom Kingdom; Peach has been captured; Queen Bean, who was visiting Mushroom Kingdom, was assassinated by Fawful; all Pokemon have been put in stasis in airtight Poke Balls; Wario turned good after Waluigi was killed by Bowser; Shroobs have invaded Beanbean Kingdom; and all other Yoshis have been enslaved or turned into Yoobs. Yoshi is horrified, but Mario tells him that there is still some chance that the kingdom can be saved. Once again, Reality tears.
The chapter opens at night, as Mario, Yoshi, and Luigi are getting a good night's rest. Luigi hears a rustling noise outside, and goes to investigate. when he peers into the bushes, there is a flash of light that Luigi vanishes into with a scream. Yoshi runs down to see what was wrong, but Luigi is just sitting there happily and says that he was "um, just checking the flowers! Right, right..." Yoshi doesn't believe him, but goes back to bed. The moment Yoshi disappears upstairs, Luigi transforms into a Dry Bones-like Dimentio. Dimentio/Luigi summons an army of Dry Bones to attack the apartment. Yoshi and Mario fight through them, and try to confront Dimentio/Luigi but he escapes in a hot air balloon. Reality rips some more.
Mario and Yoshi decide that the only way to defeat Luigi/Dimentio is to free the Pokemon. They head to the base where they are being kept. Mario and Yoshi defeat the guards and release all of the Pokemon. One Pokemon, a Snorlax that had been mutated, attacks the two. They beat him and set the Pokemon loose. Reality is seen ripping more.
The chapter opens as the Dimentio/Luigi creature lands the hot air balloon at Fawful's HQ. It enters and tells Fawful that the mushroom kingdom will never be his. Fawful is enraged, but Dimentio/Luigi cuts a giant chandelier from the ceiling, crushing the mad bean. He croaks out "I... have... fury..." before dying. Dimentio/Luigi turns around to see an army of Pokemon heading straight for him. As they trample him, reality shreds itself apart more and more...
The chapter opens as Mario suddenly feels that Luigi is dead as reality rips around him. He becomes enraged and blames Yoshi for it, for no reason. He tries to strangle the little dinosaur, but Yoshi sees one of the reality rips and shoves Mario in. Time quivers, and reality begins coming apart more and more until finally Yoshi is sucked in as well.
The chapter begins as Mario, Luigi, and Yoshi are standing in space. Bewildered, they try to find out where they are when A glowing figure appears before them and introduces itself as Light. It says that this was not the fate that Mushroom Kingdom was meant for, so this time must come to an end. Luigi is confused, so Light explains. Time has hundreds of alternate time lines, and one main time line. The main time line was originally going to be that Mario married Peach and everyone would live happily ever after. But when Mario accidentally killed Dimentio (see Prologue pt. 2) the main timeline shifted, becoming one of tragedy. The only way to revert the timeline to the original main timeline- the happy one- is to obliterate this Time line entirely. Mario, Luigi, and Yoshi return to the unhappy timeline and widen the reality rips, thus entirely obliterating that time line. It never happened now; Bowser never owned Mushroom Kingdom, Queen Bean was never assassinated, Luigi was never possessed by the spirit of Dimentio. None of it ever happened, and never will.
Epilogue, pt 1
The chapter opens in the present. The Super Mario Bros. are building a time machine, however this time, Yoshi does not fall in.
Epilogue, pt 2
The chapter opens ten years into the future as a 3-D Dimentio, having used absorbed the void, wrecks Mushroom Kingdom. Mario and Luigi try to stop it, but are battered and hurt. Finally, after a long battle, the bros. beat Dimentio and but don't kill him this time. Instead they lock hm up, and live happily ever after.