In Super Mystery Dungeon, there are 20 different Pokmon that the player can start as, which includes all of the starter Pokmon of the main regions up to Generation VI, as well as Pikachu and Riolu. After taking the Pokmon Quiz in the beginning of the game, the player is able to either accept the Pokmon the quiz selected, or deny it to choose a different one. Similarly, the game will also choose the partner Pokmon, but the player is able to choose another. However, same as the previous Mystery Dungeon games, when choosing a new partner, one is unable to choose a Pokmon which is the same type as the player.
The Player awakens alone in a forest with no memories of who they were except their name. While getting a drink of water, the Player discovers they have been transformed into a Pokmon. A trio of Beheeyem find the Player and begin attacking them, forcing the Player to flee. While running, the Player finds a Nuzleaf walking about, who ends up fleeing with the Player when the Beheeyem attack him as well. The two are forced to travel through a mystery dungeon to escape the Beheeyem and Nuzleaf instructs the Player on how to navigate dungeons.
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After traveling dungeon for a bit, the Player explains their amnesia and transformation into a Pokmon to Nuzleaf, but the Beheeyem begin catching up and force them to keep moving. Once they exit the dungeon and making sure they lost the Beheeyem, Nuzleaf offers to let the Player stay at his home for a bit when he learns they have nowhere to go. Nuzleaf takes the Player to his home in Serene Village.
Nuzleaf brings the Player into his house and sets up a room for the Player. He warns the Player not to tell anyone else about the Beheeyem for fear of stirring up a panic and decides to enroll them in the village school before leaving to attend to an errand. The Player hears someone hanging around the house and, fearing it might be the Beheeyem, leaves to investigate. They discover the noise was actually coming from the Partner takes them on a forced trip around the village. The trip is cut short when the Partner is caught by several Pokmon they annoyed through their antics and is brought home by their caretaker, Carracosta.
While exploring the village, the Player finds a Deerling demanding a Shelmet to take her to their friend Goomy, who went off after being pressured by Shelmet and his friend Pancham. The Player follows them and finds, Deerling, Shelmet, and Pancham arguing about the latter two pushing Goomy into exploring a dungeon alone to retrieve something they lost. The Player offers to find Goomy and goes into the dungeon to search for him. They find Goomy with the sheet of paper he was supposed to retreat and brings him back. Even though Pancham and Shelmet leave after teasing Goomy some more, Deerling compliments his courage and thanks the Player. That night, Nuzleaf learns of the Player's adventure, and though angry at first, allows the Player free reign of the village. The next day, Nuzleaf takes the Player to their first day of school.
Nuzleaf introduces the Player to the school principal, Simipour, and vice principal, Watchog, before leaving the Player to their first day of school. The Player is introduced to their classmates, most of whom are the Pokmon the Player met yesterday, and the Partner arrives late for class and accidentally crashes into the Player, knocking them out. After waking up and finishing class, the Player heads home with the Partner accompanying them. The Partner offers to show the Player a special place, but before he can take them there, the two are approached by Pancham and Shelmet. The challenge the Player to explore a difficult place.
They take the Player and Partner to the Drilbur Coal Mine that is also a mystery dungeon. They challenge the Player to travel down the barred left path of the mine and bring back red stones as proof of their bravery. The Partner offers to go as well, unaware the whole challenge is a prank, and the two enter the dungeon after tricking the Drilbur hanging around the entrance. When the two reach the part of the mine that splits off, they head down the barred left path. Upon reaching the bottom of the dungeon, they are found by a Gabite who declares the two are trespassing in his territory and when the Partner explains that they came for red stones, he declares the stones are his treasure and attacks. After Gabite is defeated, the Drilbur, who are actually his underlings, ask him to hear the two out and Partner explains they never intended to steal anything. Realizing he acted rashly, Gabite shows the Player and Partner to his jewel collection as an apology. He explains that more Pokmon kept taking his jewels, so he had the Drilbur block off the passage. Satisfied with the adventure they had with the Player, the Partner leaves with the Player empty handed and the two return to Serene Village. When Pancham and Shelmet ask about the red stone they were supposed to bring, the Partner explains they bring back any stones since they were so important to Gabite.
Afterward, the Partner takes the Player to the special place they mentioned earlier, a hilltop with a view of Serene Village. The Partner expresses their dream to become an explorer and have adventures in the world by joining the Expedition Society. However, kids aren't allowed to join the Expedition Society, but the Partner hasn't given up and vows to achieve their dream. That night, the Player wonders why they are in the Pokmon world and how they were turned into a Pokmon. Meanwhile in the atmosphere, Rayquaza flees after discovering something and feels true fear at it's threat.
The next morning, the Player wakes up to discover Nuzleaf left a note explaining that he will be gone for a few days. They head to school with the Partner where Farfetch'd announces there will be a field trip that day. The class is split into groups of three to retrieve flags from the dungeon behind the school and the Player is grouped with the Partner and Goomy. The two teams are given items for the field trip and make their way through the dungeon with the telepathic help of their classmate, Espurr. The Player's team makes it to the flags first, but get separated from Goomy and are sent back to search for him. After Goomy is found and class ends for the day, the Partner becomes depressed at the consequences of their reckless behavior, unaware someone is listening in.
The next day, the Player finds the Partner arguing with Pancham and Shelmet about the Partner wanting to join the Expedition Society, but the Partner refuses to be depressed over Pancham and Shelmet's teasing. During class, Vice Principal Watchog leads another dungeon outing to teach the students about Emeras and Looplets. The Player is teamed up with Espurr and Deerling to complete the Glittering Mountain dungeon. When the Player's team reach the end of the dungeon, they discover they are the first to arrive and pass the lesson (while the other team is given extra work for their terrible teamwork). After class, the Player heads home with Deerling and Goomy and they discuss their frustrations with the Partner's reckless behavior, causing the Player to realize the Partner isn't very close with the other kids.
The next day, the Player discovers Nuzleaf has returned before leaving for school. On the way, they see some Pokmon discussing the start of Honey Season where Beedrill and Combee begin making delicious honey in Nectar Meadow, though they tend to become tense during the honey making. When the Player gets to class, Pancham asks them where they came from and the Player decides to tell the truth about them being from the human world, though their claim is dismissed. Later, the class is given a lesson with the police, Magnezone, Magneton, and Magnemite, providing instruction of how to use a team attack called an Alliance.
The next day, the class on Evolving is interrupted by a Roselia, who is searching for her missing child Budew, but she collapses from a dizzy spell and is taken for treatment by Nurse Audino. The Player remembers seeing Budew the previous day overhearing the discussion about Honey Season and suspects she went to Nectar Medow. The Players tells this to the rest of the class, but Pancham believes they are lying, so the Player goes off alone to find Budew. Before they can leave for Nectar Meadow, the Partner catches up to them and explains that they believe the Player and goes with them to find Budew.
Budew reaches the end of Nectar Meadow, but the local Beedrill and Combee believe she has come to steal honey. The Player and Partner arrive to protect Budew and defeat and Combee and Beedrill. The Combee and Beedrill refuse to give up until their leader Vespiquen appears to investigate the ruckus and stops them, knowing the children are not thieves. She apologizes to the Player, Partner, and Budew for the misunderstanding and Budew explains she came to buy some Honey because she thought the nutritious Honey would help her mom get better since she was feeling unwell. Vespiquen gives Budew some Honey for free as a gift and she returns home with the Player and Partner.
That night, Budew is reunited with her mother on the hilltop, who gives the Player and Partner her gratitude. Before the Player returns home, the Partner tells them that they believe their story about being a human and asks to be their friend so they can support each other. When the Player agrees to be the Partner's friend, the Partner give them a scarf, one of two they were wrapped in as a child before their guardian, Carracosta, found them and adopted them.
While heading to school with the Partner, the Player finds the Ampharos stumbling around. Ampharos introduces himself as an explorer (but with the worst sense of direction) before stumbling off, accidentally dropping a crystalline orb. The Player and Partner pick up the item and decide to give it back to Ampharos after class. After sneaking past Watchog, who is mad the Player and Partner left school yesterday, with Espurr's help, Principal Simipour explains that Roselia told her about the incident at Nectar Meadow and excuses them from punishment, leading to the other classmates giving them respect. 152ee80cbc