During the events of MOTHER, her mother has gone missing, so she resides with her father in the Snowman Chateau. When spoken to by Ninten for the first time, she recognizes him from a dream she recently had. When Ninten returns her hat to her, she asks him a question concerning his name and thereafter mentions that her mother is missing and that she needs his help finding her, suggesting that they should go to Youngtown as their first destination. She vows to her father that she will eventually return with her mother, and then joins Ninten's and Lloyd's party, equipped with her newly retrieved hat.
Instead of going to Youngtown, the party travels to Spookane, a town which has been infested by various harmful creatures. They obtain a key from a female resident, which gains access to her house, being infamous for the ghost-like beings that inhabit it. Inside of the house, the party discovers a piano that plays a tune by itself, being the fourth melody that Ninten comes across in his search after eight specific melodies.
The party heads off to Union Station by train, where they continue on to Yucca Desert on foot. In the desert, the party happens upon a cactus that possesses some facial traits; when using Telepathy on the cactus, it will sing the fifth melody, which the party memorizes. After purchasing ten ticket stubs from a man in the desert, the party is rewarded with his tank. While navigating the tank, the trio encounters a giant robot at the entrance of a ruin. Protected inside the tank, they manage to defeat the robot, although the tank is destroyed in the process. After walking through the labyrinth-like ruins, the party reaches a cave inhabited by a strange, pink object that teleports them to Magicant.
They head off to the Magicant Underground in the eastern portion of the land, where they meet a dragon, whom they are engaged in a battle with. After defeat, the dragon croons a tune, being the sixth melody that is memorized by the party. The trio exits the underground and is teleported to a cave nearby Youngtown. In Youngtown, nearly all the grown-ups have disappeared, leaving all the children in fear and panic. After Ana and Ninten learn Teleport by a toddler in the town, the party continues to the swamp to the east.
After traveling across the swamp, they reach Ellay, a city notorious for the criminal Bla-Bla Gang, whose members roam around the city while displaying hostile behavior. The party goes into the Live House after purchasing a ticket, where they get to perform onstage. Once the performance is over, they are confronted by the leader of the Bla-Bla Gang, Teddy, who accuses them of beating up on his gang members, followed by a battle between him and Ninten. Teddy quickly ends the battle however, and instead asks them to help him avenge the death of his parents. He takes Lloyd's place, thinking of him as weak, and then the party heads off to Mt. Itoi, being the location where his parents died.
After having progressed up the mountain for a while, the party finds a house, inhabited by a healer, who heals the entire party without any cost. Teddy temporarily leaves Ana and Ninten to themselves, as he has a few phone calls to make. In a separate room of the house, Ana confesses her romantic feelings for Ninten, and the two of them dance with each other. They are however interrupted by Teddy, who says that it is time for them to leave. They are subsequently attacked by another giant robot, who easily defeats them all. Everyone is saved by Lloyd who shows up in a tank, and transports them all to a house at the base of Mt. Itoi, where they are treated by a doctor. Teddy did unfortunately suffer more grave injuries from the attack and cannot continue to travel with Ana and Ninten, and is instead replaced by Lloyd.
The party travels up the mountain once again, and does this time find a lake, with an accessible boat nearby. They embark the boat, and are before not too long sucked into a hidden building at the bottom of the lake. It is the residence to a robot named Eve, who, when spoken to, says that its purpose is to protect the three of them. The building then collapses, and all of them end up on the shore of the lake. The party goes further up the mountain, until they suddenly get attacked by a third gigantic robot. The robot manages to defeat Eve, but does also get destroyed due to the explosion caused by Eve's death.
Near the highest accessible point of the mountain, the party comes across a tombstone. When they approach it, a crystal appears in front of them, and does after a short speech reveal the eighth melody, followed by it making a disappearance. With all of the eight melodies retrieved, the party heads off to Magicant. They show the melodies they have learned to Queen Mary, being the person who requested Ninten to gather all the melodies. After hearing the song, she remembers it and starts to sing it herself. Queen Mary also retrieves her memory thanks to the song, and Magicant is then revealed to be an illusion caused by the consciousness of Ninten's great-grandmother. The entirety of Magicant disappears, all that is left being a barren wasteland, and the party is automatically teleported back to the tombstone they found earlier.
They enter a nearby cave, and find that a portion of the cave is filled with humans trapped in capsule-shaped objects. One person who is trapped recognizes Ana and says that her mother is trapped in a room further back. The party walks into a deeper segment of the cave, and enters a portion of it where an ascending ship appears in front of them. Giygas, the creature who has caused the various ominous occurrences throughout the party's journey, is revealed to be inside of it, and engages a battle with the party. The trio manages to defeat Giygas thanks to the song they have recently learned, and Giygas disappears toward the sky.
After having successfully gotten rid of Giygas, Ana is reunited with her mother, as the party saves all the people that were trapped inside of the capsules. Ana can later be seen taking farewell of Ninten and Lloyd, before entering her chateau. In another segment, she reads a letter that she has received from Ninten, where she hopes that they will meet each other again soon.
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