After being summoned to the palace by Toad, Mario and Luigi confront Bowser, who coincidentally was just attempting to kidnap Peach. Mario easily subdues him, and learns that Peach's voice was stolen by Cackletta, and replaced it with explosive speech.
Bowser decides not to kidnap her now, and teams up with Mario to retrieve her true voice back from the Beanbean Kingdom, with the intention of kidnapping her later when she won't destroy his castle with explosives.
Mario, Luigi, and Bowser fly to the Beanbean Kingdom via Bowser's new airship, the Koopa Cruiser. Mid-flight, Fawful attacks the cruiser and blows it out of the sky. In the aftermath, Bowser is separated from the brothers, who continue their mission alone.
Whilst on the journey, the brothers rescue Prince Peasley, who had been captured by Cackletta and Fawful and turned into a monster. The brothers reach Beanbean Castle Town in ruins from an attack by Cackletta, and step into a trap laid by Cackletta in disguise, who drops them into the sewers.
Within the sewers, the brothers free some of the castle's residents, who warn that Cackletta's goal is to steal the Beanstar from the castle, which once awoken with Peach's voice, will grant all of Cackletta's wishes.
When the brothers try to stop Cackletta, she attacks them with a mutated form of Queen Bean of the Beanbean Kingdom and escapes. After defeating the Queen, Mario and Luigi travel to Chucklehuck Woods to retrieve the Chuckola Reserve, a soda which will restore Queen Bean. On their journey, the brothers encounter Popple, a thief also after the Chuckola Reserve, accomplices by an amnesiac Bowser (referred to as "Rookie"). After defeating them, the brothers obtain the Reserve and return to Beanbean Castle Town.
With Queen Bean cured, Mario and Luigi travel to Woohoo Hooniversity, where Cackletta plans to awaken the Beanstar. Upon being exposed to Peach's voice, the Beanstar goes berserk. Mario and Luigi then reach and severely injure Cackletta, so that Fawful must suck up her soul in his "vacuum helmet" to save her life. Cackletta commands Fawful to attack, but he is stopped by Prince Peasley, who knocks him with his sword out of Woohoo Hooniversity. When going to retrieve the Beanstar, they run into Popple and "Rookie" again. After defeating them, the Beanstar is accidentally exposed to Peach's voice and goes berserk again, shoots into the sky, and explodes into four pieces, which scatter across Beanbean Kingdom.
The brothers return to Beanbean Castle, where they discover that Peach's voice had never been stolen. Prince Peasley learned of Cackletta's plot and warned the Princess beforehand, so they disguised Birdo as Peach, who had her voice stolen instead of the real Peach, explaining the Beanstar's reaction to "Peach's" voice. Peach had been unable to tell the brothers the truth, due to Bowser's presence. Meanwhile, Fawful imbues a weak Bowser with Cackletta's soul, resulting in the twisted Bowletta.
On a trip to Little Fungitown, a community of Toad immigrants, Peach is kidnapped by Bowletta, who demands all pieces of the Beanstar in exchange for Peach. After retrieving the Beanstar, Mario and Luigi travel to Joke's End, an arctic palace off the coast of the Beanbean Kingdom, to make the exchange. Bowletta, as expected, refuses to hand over Peach, but Mario pulls off a double-bluff that results in Luigi, disguised in Peach's spare dress, being taken in Peach's stead. He is taken aboard the repaired Koopa Cruiser, but manages to escape, retrieving the Beanstar in the process. Upon returning to Beanbean Castle Town, the brothers discover it to be under attack by Bowser's flying castle, which has been taken over by Bowletta. The brothers and Prince Peasley fly up to it to stop Cackletta once and for all.
In Bowser's Castle, Mario and Luigi battle past the Koopalings and Fawful before making it to Bowletta. Feinting defeat, she knocks them out from behind with a Bob-omb, and swallows them both. After waking up in her belly, the brothers conquer Cackletta's soul for good, returning Bowser to normal. Afterwards, the brothers escape the castle before it explodes from a bomb set by Peasley. After the explosion, the castle falls into the ocean, with the Mario brothers having saved both the Beanbean Kingdom and the Mushroom Kingdom.
|Mario||Mario, along with Luigi, will go off to find the culprit who took Peach's voice.|
|Luigi||Luigi is Mario's brother, and will usually be too frightened to go on adventures.|
|Princess Peach||In the game, Peach's voice has been stolen by Cackletta and you need to get it back.|
|Cackletta||Cackletta, the evil witch stole princess Peach's voice so she could use it to awake the power stars that will grant any wish of a perfect voice.|
|Prince Peasley||Queen Bean's son, and the character who will help out the brothers throughout the game.|
|Bowser||Bowser will assist to you through the first half of the game, when he then gets taken under control of Cackletta and Fawful.|
|Queen Bean||The Queen of Bean Bean Kingdom.|
|Yoshi||The Yoshi's all visit the Yoshi Theater which is made just for them.|
|Toadsworth||Peach's longtime protector.|
|Mario RPG series|
|Super Mario RPG series||Super Mario RPG: Legend of the Seven Stars|
|Paper Mario series||Paper Mario • The Thousand-Year Door • Super Paper Mario • Sticker Star • Color Splash|
|Mario & Luigi series||Superstar Saga (Bowser's Minions) • Partners in Time • Bowser's Inside Story (Bowser Jr.’s Journey) • Dream Team • Paper Jam|
|Mario + Rabbids series||Mario + Rabbids: Kingdom Battle|