From the Super Mario Wiki, the Mario encyclopedia
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In the Mario franchise, a wish is a strong hope or desire. Wish-granting is tied to Stars, with Super Mario RPG: Legend of the Seven Stars even revealing that wishes turn into physical Wish Stars when they reach the Star Road, which then fall back to the earth as shooting stars after they are granted. In Paper Mario, it is revealed that the Star Spirits choose which wishes to grant based on the integrity of the wisher, with selfish wishes never being granted. Wishes have also been shown to have a direct effect on the world during some of Mario's adventures, such as counteracting and weakening the powers of the Shadow Queen in Paper Mario: The Thousand-Year Door. It was also speculated by the Star being Geno that without the power of wishes and the Star Road, Mario might be unable to rescue Princess Toadstool from Bowser.
Super Mario RPG: Legend of the Seven Stars
During the events of Super Mario RPG: Legend of the Seven Stars, the Star Road is shattered into seven Star Pieces by the giant sword Exor as part of the invasion by the Smithy Gang from another dimension. As a result, no wishes can be granted: no new wishes are made into Wish Stars, and existing Wish Stars fall down to Star Hill despite not being granted. The situation was so dire, the stars sent one of their own, Geno, to assist Mario in collecting the pieces of the Star Road. As explained by Geno, without the Star Road granting wishes, peace could not return to the the world so long a theirs was "a world where wishes can't come true anymore."
Along with Toadstool, Bowser and Mallow, Mario and Geno collect six of the Star Pieces and confront Smithy, who has the last piece. Upon learning of the power of the Star Road, Smithy resolves to keep the piece for himself, and replace wishes with weapons as the dominant force in the world. In the end, however, Smithy was destroyed in battle and the Star Road was repaired, and the power of wishes was restored to the world.
Paper Mario series
Paper Mario reveals that the power of wishes has existed in some form since the beginning of time, with the Star Spirits in Star Haven watching over the world below and granting wishes to deserving people, thus allowing the world to prosper peacefully. Because Bowser's wishes were always selfish, they were never granted, and in the outset of the game, he attacks Star Haven and steals the powerful Star Rod in order to grant them himself. Using the power of the Star Rod, he traps the Star Spirits in playing cards, kidnaps Princess Peach and her entire castle, renders himself invincible and even defeats Mario initially. Fortunately, Mario is able to free the Star Spirits and face Bowser once more, and once Peach wishes for the Star Spirits' power to increase, Mario is able to defeat Bowser using the Peach Beam, and the authority to grant wishes via the Star Rod was returned to the Star Spirits.
Paper Mario: The Thousand-Year Door
Wishes play a much smaller yet still vital role in Paper Mario: The Thousand-Year Door. During the final battle, the Crystal Stars fly across the land and begin transmitting the wishes and positive energies of the people he met on his journey, which then weaken the Shadow Queen enough for Mario and his partners to be able to deal damage. Before the wish powers intervene, like Bowser in the last game, the Shadow Queen is invulnerable to attacks.
Paper Mario: Sticker Star
In Paper Mario: Sticker Star, the Sticker Comet holds the wishes of all the citizens of the Mushroom Kingdom. At the start of the game, Bowser attempts to steal the comet to grant his own wishes, causing it to shatter into Royal Stickers. Several bosses, such as Mizzter Blizzard, use the Royal Stickers to grant their wishes and gain power. At the end of the game, once the comet is restored, Mario wishes for Kersti to be brought back to life, while Princess Peach comments on how disastrous the power to grant wishes without wisdom can be.
Paper Mario: Color Splash
Wishes play a small role in Paper Mario: Color Splash. After riding the Sunset Express, Mario and Huey reach Starlight Cape. Mario wishes on a shooting star for Princess Peach to be safe, while Huey wishes to recover every Big Paint Star. After they make their wishes, the Orange Big Paint Star appears, allowing Mario to reclaim it and end the level.
Paper Mario: The Origami King
Wishes play a major role in King Olly's plan in Paper Mario: The Origami King. One of his goals includes folding a thousand origami cranes to make a wish using the Thousand-Fold Technique to turn all Toads into blank pieces of scrap paper as a means of revenge on his creator apparently scribbling on him. Upon his defeat, Olly learns the truth and feels remorse for his actions, and Olivia folds his body into the thousandth crane to undo all of his origami-folding, including herself.
Mario & Luigi series
Mario & Luigi: Superstar Saga
The Beanstar from Mario & Luigi: Superstar Saga has the power to grant wishes to the one awakening it with a pure, sweet voice. Cackletta plans to use Peach's voice to awaken it and grant her wish of ruling the kingdom, but due to her plans being foiled beforehand the Beanstar shatters into pieces instead. Its power is never demonstrated in-game.
Mario & Luigi: Bowser's Inside Story
Wishes play a very minor role in Mario & Luigi: Bowser's Inside Story and its remake, Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey. At the start of the game, Princess Peach uses Wish Power to decrease Bowser's power, then levitate and toss him out of the castle.
Mario & Luigi: Dream Team
Wishes play a larger role in Mario & Luigi: Dream Team. The Dream Stone can grant wishes, as could its destroyed counterpart, the Dark Stone. Bowser and Antasma steal the Dream Stone and use its power to create Neo Bowser Castle. The Dream World of the castle has minor wish-granting properties, as Bowser becomes gigantic and summons obstacles for the Mario Bros. to combat.
At the end of the game, Bowser attempts to use the Dream Stone to erase Mario and Luigi from existence, but Peach and Starlow use their combined Wish Power, described as the power of good thoughts, to shatter the Dream Stone. Bowser then inhales the pieces and becomes Dreamy Bowser, granting him a large power boost and the ability to perform normally-impossible feats, such as cloning himself or creating minions out of nothing.