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Mario and Luigi are at home, when Parakarry comes and delivers the mail. Luigi goes and grabs it and comes back in. He reads the letter:
Dear Mario and Luigi,
Tonight I am holding a party to celebrate the new alliance we have formed with the Aether Kingdom. I will be waiting at my castle. Don’t be late, or you’ll miss the fireworks. From, Peach.
Mario and Luigi head to the castle and enter its doors. Now you can play as Mario. Ascend the castle and meet Peach at the top. Suddenly, Bowser smashes through the window, holding a black scepter. He tells Peach to come with him and nobody will get hurt. She refuses, so Bowser aims the scepter at Peach, but Mario jumps in front and challenges him.
Bowser will slash you with his claws for 1 damage. Peach tells Mario to use action commands to defend and power up his jump and hammer attacks. Bowser should fall easily.
After defeating Bowser, he uses his scepter to teleport back to his castle. Merlon, who watched the entire battle, walks up to Mario and tells him that he has seen the scepter that Bowser had before.
He explains that the scepter is called the Ebony Scepter and that whoever wields it has infinite power over darkness, and that the only way to counteract it is to use the Rainbow Orbs, that lie in the Rainbow Shrine on the outskirts of Koopa Village.
Mario exits the castle and heads into Toad Town. The title screen appears and now you gain control of Mario. You can explore Toad Town if you wish, such places to visit are the Item Shop, Inn, Train Station, Post Office, and The Dojo.
South of the central plaza lies the entrance to Forever Forest, which is blocked off for now. Tayce T. has gone on holiday, but her cousin Muss T. is looking after her house and he will kindly offer to cook any items you give him, but he can only cook one item at a time for now.
The train station and the docks are currently blocked off, the archway to Flower Fields is inactive, the way to Goomba Village is inaccessible for the whole game, the pipe to Toad Town Tunnels is temporarily blocked and the gates to Forever Forest are locked.
Head east out of the main plaza that leads to Pleasant Path and you will be stopped by Luigi, who exclaims that this time he is not going to be left behind this time, and he joins your party! His field ability is to perform a high jump with Mario, to reach new heights.
Proceed along the path, defeating numerous Goombas and Koopas along the way, until you reach Koopa Village. The path to the Koopa Bros. Fortress is inaccessible.
Upon entering the village, you will see the town being attacked by a black, shadow version of Bowser. It sees you and runs away. Follow him through the village and through the pathway beyond it.
Continue down the path to reach the Rainbow Shrine. There, the shadow will engage in battle with you.
Boss: Bowser's Apparition
This battle is almost the same as the first battle with Bowser. The Apparition will slash you with his claws for 2 damage.
After defeating it, the shadowy apparition disappears into nothingness. When you enter the shrine you see that the Rainbow Orbs are gone. Merlon will telepathically communicate Mario and tells him to return to Toad Town. A pipe will appear near you, enter it.
You will now be in front of Merlon’s House in Toad Town, go inside. He tells Mario that he had a vision of Bowser stealing the Rainbow Orbs from the shrine and giving them to his minions. He says that he is feeling the power of one of the Rainbow Orbs coming from Flower Fields. He uses his magic to activate the archway to Flower Fields and tells Mario good luck. Stock up at the store and enter the portal to Flower Fields.