Ninten displays few distinct traits and little personality throughout the game, due to him having the role of a typical silent protagonist. He has only one sentence of actual dialogue in the entire game, being in the ending sequence of the game, where he merely states that it would be nice to have some rest, as the Earth's crisis is over. He is however shown to be the only main character in the game who is asthmatic, being a property which affects him negatively in-game if he is exposed to exhaust gases, and can only be cured by the use of Asthma Spray. He and Ana are also the only party members that can utilize PSI, although Ninten is only capable of using defensive PSI moves. His main weapons are Baseball bats, being the only items in the game that are unique to him, and which is also a trait that is succeeded by Ness in EarthBound. His personality has been expanded and elaborated on in several guides and books, though the degree of canonicity in these are debatable.
In Encyclopedia Mother, he is depicted as an energetic and adventurous boy, being compared with Indiana Jones. His dog, Mick, is very close to him, especially during his years as an infant. He is very popular in school, and has been chosen as "Mr. Leader" by his fellow classmates. He also displays a strong interest in baseball, being a "team regular" in the boys' baseball team, and thus plays baseball routinely. Being kept a secret from his mother, he enjoys playing the electric guitar that his father has gotten for him, especially when being accompanied by Mick. His favorite food is prime rib, which his mother serves for dinner once a week. Ninten also loves penguins, even owning a penguin toy, which is one of his most cherished possessions.
Among Ninten's favorite things are his baseball cap, a ticket to the Tokyo Giants, a photo of his great-grandmother, a ball signed by Shigeo Nagashima, a bent spoon, and a penguin toy. He got the baseball cap from his father, and it is considered to be his trademark; he rarely takes it off, being mainly when he showers, when it comes off as a result from a powerful swing when playing baseball, or when he sleeps, as can be seen in the expanded ending of Mother. The Tokyo Giants tickets were brought to him by his father after a trip to Japan, which Ninten believes is the "sister team" of the San Francisco Giants, being his favorite team. The sepia-colored, elliptical-bordered photo of his great-grandmother is kept in his desk, and is something he really treasures. The right half of the photo, which is thought to depict her husband, George, has been torn off. Ninten received the ball signed by Shigeo Nagashima when he was watching a match in the "big leagues", and thereafter noticed that Nagashima sat next to him, recalling him from a special feature in a baseball magazine. The bent spoon became curved when he played with it during a dinner, when he already was full due to earlier having eaten at a hot dog stand, and as a result was unable to restrain himself, and bent the spoon through unknown means. Lastly, Ninten keeps the penguin toy due to his interest of penguins. When penguins were introduced at the local zoo, it made a really big impression on him, as he previously only had seen them on pictures and TV.
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The game starts off with Ninten's home being invading by a poltergeist. Several inanimate objects are brought to life during the paranormal phenomenon, including lamps and one of Ninten's sisters' dolls. After defeating the doll, he finds a music box inside of it, which starts to play a melody, whose significance is left ambiguous, but still is memorized by him. After the event is over and the poltergeist has disappeared, Ninten gets a call from his father, who vaguely expresses that it is time for Ninten to go on "a little adventure" in order to explore the potential of his powers. He also tells Ninten that there is something in the house's basement that might assist him during his journey, although he has forgotten where he put the key that is needed in order to make it accessible. After Ninten has retrieved the key from his dog and obtained his great-grandfather's diary from the basement, he initiates his journey by heading to the closest town, Podunk.
On the way there, Ninten spots a woman in panic in front of her home. Asking what is wrong, the woman tells him that her daughter, Pippi, has gone missing. He continues into town and learns that several odd occurrences have struck the settlement; poltergeists intruding people's homes, zombies roaming around in the town, animals that are running amok in the town's zoo, and a girl who is lost somewhere in the cemetery. After talking to the mayor of Podunk, he implores Ninten to rescue the missing girl. Ninten eventually finds her in a casket deep inside of the cemetery. Pippi shows a liking to her rescuer, giving him a Franklin Badge if he acknowledges his bravery and modesty. Going back into town and leaving Pippi in the hands of the mayor, Ninten and Pippi part ways. The mayor then requests him to go the zoo, hoping that he will take care of the issues occurring there.
Before heading to the zoo however, Ninten takes a stop at the town's department store. When going to the top floor he is informed that all the animals but a canary chick have escaped from the store. The salesman tries to sell Ninten the chick for $85, but if refused, it will be received for free. The chick is taken to Canary Village to have it returned to its mother. The mother, named Laura, ecstatic about her returned chick, sings another melody that Ninten memorizes, being the second one. He then continues on to the zoo.
When entering the Choucream Zoo, Ninten will encounter many hostile animals and walk in a snake-like pattern before reaching the Superintendent's Office in the eastern portion of the zoo. Here, he will engage a battle with Starman Jr. after examining a capsule-like object on the building's top floor. When it has been defeated, the odd sound that is revealed to be the reason for the animals' strange behavior disappears, turning the zoo into its original state again. Within one of the zoo's fences resides a monkey, who sings the third melody when a sign attached to the fence is read.
Even though no reward will be given from the mayor for the deed, a cave to the east of the zoo will become accessible. Inside of the cave, Ninten will come across a strange rock-like object, that telepathically will ask him a vague riddle-like question. When he finds a corresponding answer in his great-grandfather's diary, and then says it out loud, he will be transported to the mysterious land of Magicant. Upon entering a castle in the northern portion of Magicant, Ninten will meet the the governing figure of the land, Queen Mary. She requests him to retrieve the eight notes of a song, which she herself has forgotten, and then return to sing it for her. Ninten then exits Magicant through an underground maze, and is sent to another rock-like object located inside of a cave.
After exiting the cave, he discovers that he has been teleported to the outskirts of Merrysville. Inside of the town's elementary school, Ninten meets a boy hiding in a trash can on the school's roof. He refuses to come out of the bin, fearing that the other students will continue to pick on him, but eventually gathers enough courage to leave the bin, and then introduces himself as Lloyd, followed by him saying that he would like to fly a Bottle Rocket. In a factory to the south, Ninten manages to find a Bottle Rocket, being located in a trash can, which he picks up. When shown to Lloyd, he becomes excited for finally having a Bottle Rocket in his possession, and thereafter leads Ninten to the school's lab, and does after a failed experiment, involving the Bottle Rocket, join Ninten on his journey.
The duo heads to Duncan's Factory, where they thanks to Lloyd manages to activate one of the factory's rockets, which they do in order to get rid of the rocks obstructing the way to Union Station. When the station becomes accessible, the two of them take a train to Reindeer, where they meet an old woman, who gives them a hat, believing it to be the property of a girl in Snowman. After showing the hat to a girl named Ana, who lives in a chateau in the eastern portion of Snowman, she will tell Ninten that he is the boy that she has seen in her dreams and who will help her to find her lost mother, and thereafter joins Ninten and Lloyd on their journey.
The three of them take the train to Spookane, which is shown to have been overrun by malevolent animals and alien-like beings upon their arrival. They head to the inhabited portion of the town, where people express worry concerning the current circumstances, not only being concerned about the creatures that have infested the western portion of the town, but also the ghost-like creatures that have assumed control over the house of the Rosemarys. Ninten is entrusted with the key to the house by the mother of Rosemarys, being certain that Ninten will get the place back into normal. Deep inside of the house, Ninten and his friends find a piano that plays by itself, and that plays the fourth melody when checked.
The party returns to Union Station, where they discover that a small portion of the tracks leading to the east are demolished, making it impossible for the train to transport them beyond that point. They do instead make a detour around the cliffs north of the tracks, leading to them ending up in Yucca Desert. In the desert, the party come across a cactus with some facial features. After using Telepathy on it, it will start to sing the fifth melody. To the east of the cactus resides a man, who will let Ninten and his friends borrow his tank once they have obtained ten Ticket Stubs, which can be purchased from him from prices between $5 to $15. After the tank has been obtained, the party heads further to the east, to the Ruins of Desert, whose entrance is guarded by an enormous robot that must be battled in order to enter; the tank must however be sacrificed during the battle with it. The ruins are inhabited by various monkeys and has a maze-like layout; when the party manages to traverse the ruins and reach an entrance leading to a cave with yet another rock-like object, they will yet again be transported to Magicant.
In the Magicant Underground, a sleeping dragon resides, and Ninten should at this point have enough experience to be capable of waking it from its slumber, which will lead to the initiation of a battle. After being defeated, the dragon will reveal the sixth melody, and then go back to sleep. When Ninten exits from the underground this time however, he will be teleported to a new cave, being to the northwest of Youngtown.
Upon entering Youngtown, Ninten and his friends discover that the majority of the adults have been abducted from the town, and all of the children being in panic due to the loss of their parents. After walking around in the town for some time, the party will meet a baby that communicates with them telepathically, and who teaches them how to teleport. The party continues through the swamp to east, where they meet a Pippi, the girl who Ninten rescued in an earlier segment of the game, and who will offer them full stat recovery.
After having traversed through the swamp, the party reaches the city of Ellay, being infamous for the criminal Bla-Bla Gang, whose members can get very hostile after being interacted with. The party purchases a ticket from the city's department store, in order to enter the Live House. There, they are asked to perform onstage, where they get to dance and sing. After the party is done with the performance, the leader of the Bla-Bla Gang, Teddy, approaches them and asks them if they were the ones beating up on his fellow gang members, which is followed by a battle between Ninten and the gang leader. The battle will however break off after a couple of turns, as Teddy gets impressed by Ninten's ability to fight, calling the match a draw. He explains that he seeks vengeance for his dead parents, and kicks off Lloyd from the team, as he thinks of his ability to fight as being poor, taking his place instead.
Ninten, Ana and Teddy head off towards the base of Mt. Itoi, southeast of Ellay. They first go through a confusing maze-like set of caves, and once they have found an exit, they reach a plateau-like portion on the exterior of the mountain, where they must climb the roots of several stumps in order to progress up the mountain. Here, they will fortunately meet a healer, who will heal the entire party. Teddy temporarily leaves Ninten and Ana to themselves, as he has to make a few phone calls. A scene where Ninten and Ana dance together occurs, and ends in Ana confessing her love to Ninten. They are interrupted by Teddy, who tells them that it is time to leave; however, a loud noise appears, followed by the appearance of another gigantic robot, which is engaged in a battle with them. The party is chanceless against the strength of the robot, and faints one by one. Lloyd luckily shows up after the battle, while driving a new tank, and rescues the party by transporting them to the house of a doctor, being located outside of the entrance to Mt. Itoi. Teddy did however suffer more damage from the battle than Ninten and Ana, and is left fatally wounded in the doctor's house, while Lloyd reaccompanies the party.
The party, rejoined by Lloyd, scales the mountain yet again. After they have passed the caves and the first accessible plateau of the mountain, they reach a lake. There is a boat located near the shore, which they board. After cruising around for a while, the party reaches a portion of the lake that is affected by a whirlpool. They are then pulled down in the water by the vortex, and they all end up in a laboratory-like facility. There, they meet a robot named Eve, who is brought to life when feeling the presence of Ninten. It says that it was built by George, Ninten's great-grandfather, in order to protect Ninten. The glass windows of the facility successively break during its speech, and the entire facility ultimately breaks down, washing the entire party ashore.
With Eve in their party, the four of them continues up the peak of Mt. Itoi. When they approach the top plateau of the mountain, the party is attacked by yet another huge robot. Eve gets destroyed by the robot during the battle, however, the explosion is so powerful that the other robot is destroyed along with Eve. When checking the remains of Eve, the seventh melody is played. The party continues on, and eventually reaches the peak of the mountain, where they find what appears to be a gravestone. When examining the stone slab, a crystal appears in front of them, and starts to speak. It reveals that the love of Ninten's great-grandmother, Maria, was scattered in form of melodies, before teaching Ninten the eighth and final melody; the crystal thereafter disappears.
Ninten and his friends head back to Magicant, to show Queen Mary that they have gathered all the eight melodies. When they have sung the melodies, the queen remembers the song and starts to sing it herself. Afterwards, she and the entirety of Magicant are revealed to be illusions created from the consciousness of Maria. The queen disappears, along with Magicant, in order for Maria to join her husband among the dead.
The party is then teleported back to the gravestone at the peak of Mt. Itoi, where a cave that previously was blocked by boulders is located, but now appears to be accessible. They enter the cave and proceed through it to a deeper portion of it, where a huge ship slowly ascends, eventually leading to a battle with Giegue, the entity responsible for all the terrible occurrences throughout the game. He says during the battle that he is thankful to Ninten's family, but that the people of Earth must perish; he does however momentarily seem to offer to spare Ninten's life, which is declined by Ninten. When he has finished the speech, the party starts to sing the eight melodies, being constantly interrupted by Giegue, who tells them to stop, obviously being affected by their singing. He eventually retreats after the song has been sung repeatedly, and promises Ninten that they shall meet each other again, and thereafter flies off with the Mother Ship.
After the defeat of Giegue, the party frees the humans that have been abducted by Giegue, several of whom return to their children in Youngtown. Ninten himself returns to his home in Podunk, being greeted by his mother and sisters. He and Ana are confirmed to stay in touch by sending each other letters after the events of the game. Ninten can also be seen resting in the ending, due to the Earth's crisis finally being over.