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Mario and Luigi: Alternate Quest is a Fan-Fiction. It won't have a game come out because it's fanon, but you can buy it [not really its fanon] on the 3DS Eshop from October 8 2014 to November 9 2014.
Chapter 1: When two different dimensions Combine
This takes place after three fanon games Mario & Luigi: Alternate Dimensions, Mario & Luigi: Virtual Quest, and Mario & Luigi: Amari & Guila. It all starts out when Princess Pepper from Mario & Luigi: Alternate Dimensions goes on Fantendo and finds the game Mario & Luigi: Virtual Quest, and sees Princess Shamrock, a princess who has unlimited HP, and a slight evil Recolor of Princess Peach. Seeing that she took over the Koopa Troop, Pepper found out that Mario defeated her. She decided to go look for her to team up, and give a 1-Up Mushroom to make her back to normal. Pepper soon goes to Haunted Tower, where she finds her defeated. Pepper gives her the 1-Up Mushroom, and Shamrock comes alive again. Pepper tells her that she's from a alternate universe, and that Bowser is controling the Koopa Troop again. Hearing this, they go to Bowser's Castle and Princess Peach's Castle to take over it.
Chapter 2: Taking over Castles from Every Country in the Mushroom World
Soon with Princess Pepper successfully tooken over Princess Peach's Castle, Shamrock took over Bowser's Castle. While Shamrock also turns Bowser into stone and drops him in the lava, he actually gets sent to Roseletala's Galaxy Destroyer from Mario & Luigi: The Cosmic Duo, that happened in the past. Peach gets kidnapped in a cage that has no exit, and Pepper comes to Bowser's Castle (Now Shamrock's Castle) and meets Mario and Luigi, who has a battle to defeat them. After they defeated Mario Bros, they turn into Ram and Uil, and have another boss battle. After the two evil princesses defeat them, they team up with them, and join the conquest. Pepper went back to Peach's Castle (Now Princess Pepper's Castle) found her friends Frog, Shadow Mario & Shadow Luigi to join up too.
Chapter 3: Brainwashing is Better
After the Bros has been defeated, Ram and Uil turn back into a defeated Mario and Luigi. Pepper calls King Boo to trap Mario in a locked painting and Luigi to Mr. L, to conquer the world with them. Meanwhile, A Warp Pipe appears and Warupichi and Wareach jumps out, being shocked, they say that THEY wanted to take over the world. Wareach asks them if they can join, and Shamrock says yes, they can help them rule the world. Together, the 4 princesses goes to conquer all of it. They soon go to conquer all of the Mushroom World and defeat all the good.
Power Ups [Eshop Version]
Princess Pepper from the Chili Kingdom -She is the one that started it all. She first appeared in Mario & Luigi: Alternate Dimensions, and she wants nothing but to conquer the world With her magic power Frog Army, her minions comes to attack heroes, with villains..
Princess Shamrock from the Virtual Kingdom -The only princess with unlimited HP. She once took over the Koopa Troop, Bowser's Castle and Peach's Castle in Mario & Luigi: Virtual Quest, so shes a pro of taking over the entire planet. Now revived by Pepper, she has the power to use the Virtual Screen, making you see nothing but red and black.
Princess Wareach: You think this is the Shadow Queen Peach? Almost. Except about that nose. She thinks Wario and Waluigi is her best friends, when it's not. This is Wareach's first time taking over lands, and she gots Unlease Green Shadow to help out along!
Frogs: He's Pepper's Helpers and a big help for all of the evil princesses. He'll throw ememies at heroes, and give the player items when they are small. Blue Frog and Yellow Frog Runs shops around the area, and if you see Frogette, she'll give you a 1-Up Mushroom or a 3-Up Moon.
On October 9th 2014 [fanon], A Scribblenauts version was announced for the Wii U Eshop [fanon] coming on October 11th. This will have the same story, but a trailer [fanon] has been released and info will be shown.