Pokémon Super Mystery Dungeon

is a Nintendo 3DS game in the Mystery Dungeon series.
==New Features==
*Instead of recruiting, the player connects with other Pokémon by completing requests, displayed in the Connection Orb.
**Some Pokémon can be connected once talked to, and some can be connected along with other Pokémon at the same time.
Alliance is introduced.
*Emeras and Looplets are introduced. Putting Emeras into Looplets can give the Looplet's holder different effects, e.g. increasing stats and prevent certain status conditions.
*Mega Evolution is introduced, achieved by finding an Awakening Emera and then put it to a Looplet held by a Pokémon that can Mega Evolve. Soon the Mega Evolved Pokémon will go berserk which lasts for a few turns, but it can be prevented by an Air Looplet.
*-type is introduced.
*Wands, a type of stackable items, are introduced.
*The Progress Device is introduced that allows the player to save in a dungeon.
==Starter Pokémon==
In Super Mystery Dungeon, there are 20 different Pokémon that the player can start as, which includes all of the starter Pokémon of the main regions up to Generation VI, as well as Pikachu and Riolu. After taking the Pokémon Quiz in the beginning of the game, the player is able to either accept the Pokémon the quiz selected, or deny it to choose a different one. Similarly, the game will also choose the partner Pokémon, 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 Pokémon which is the same type as the player.
Image	Pokémon 	Type
 	Bulbasaur 	/
 	Charmander	
 	Squirtle 	
 	Pikachu 	
 	Chikorita 	
 	Cyndaquil 	
 	Totodile 	
 	Treecko 	
 	Torchic 	
 	Mudkip 	
 	Turtwig 	
 	Chimchar 	
 	Piplup 	
 	Riolu 	
 	Snivy 	
 	Tepig 	
 	Oshawott 	
 	Chespin 	
 	Fennekin 	
 	Froakie 	
==Plot==
===Main story===
A mysterious light asks the Player for help, taking them to the Pokémon world. 
Meanwhile, in the space outside the Pokémon world, a Deoxys finds Rayquaza leaving the ozone layer and realizes something is wrong.
=== Chapter 1 Those That Live On This Planet and Those That Have Come to This Planet ===
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 Pokémon. 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.
After traveling dungeon for a bit, the Player explains their amnesia and transformation into a Pokémon 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.
=== Chapter 2 Meeting the Partner ===
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 Pokémon 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.
=== Chapter 3 On a Hill Where a Large Tree Stands. ===
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 Pokémon 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 Pokémon 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 Pokémon world and how they were turned into a Pokémon. Meanwhile in the atmosphere, Rayquaza flees after discovering something and feels true fear at it's threat.
=== Chapter 4 Field Trip ===
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.
=== Chapter 5 Harmony Scarves ===
The next day, the Player discovers Nuzleaf has returned before leaving for school. On the way, they see some Pokémon 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.
Meanwhile, in the depths of the sea a Dewgong shows three Lanturn something shocking: a Wailord turned to stone.
The next day, an Ampharos arrives at Serene Village.
=== Chapter 6 A Jr. Expedition Society Member is Born! ===
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.
After class, the Player and Partner ask Kecleon about the orb Ampharos dropped and Kecleon identifies it as a Connection Orb, an item that shows the relationships between Pokémon across the world. Kecleon mentions that the orbs are carried by Expedition Society members and a Raticate reveals they saw Ampharos leave out the village gate. On the way to search for Ampharos, the pair come across Carracosta, who reveals Ampharos is heading toward Poliwrath River. When Carracosta learns the pair plan to go to Poliwrath River, he forbids them on account of it being home to a dangerous trio Pokémon called the Poliwrath Brothers. Despite Carracosta's warnings, the Partner insists of going after Ampharos and the pair head off. When the two reach the end of the Poliwrath River, they are ambushed by the Poliwrath brother. After the pair Poliwrath Brothers, the decide to look elsewhere for Ampharos, but one of the Poliwrath gets up and attacks the Players. Ampharos saves the Player and the three return to Serene Village.
That night, the Player and Parter return the Connection Orb to Ampharos on the hilltop. The Partner asks Ampharos if he is a member of the Expedition Society and Ampharos answers that he is not. The Partner explains they want to join the expedition society and Ampharos gives them and the Player Junior Expedition Badges, granting them junior membership into the Expedition Society. With the badges, the two are permitted to assist Pokémon with problems and work with them to explore dungeons. The two are also given Ampharos' Connection Orb and an Expedition Gadget to activate it. After registering the team name, the pair head home while Ampharos receives a message from a Pokémon called Dedenne who chews him out for wandering off on his own. Ampharos reports that he didn't find any problems in Serena Village and hopes he can protect that peace.
=== Chapter 7 Summer Vacation! ===
The next day after class, the Player and Partner decide to start their jobs as junior members. Before they can start, they find Ampharos stumbling around, who teaches them how to use their Connection Orb to take requests from Pokémon in need. After the pair complete a request, Ampharos shows them how to expand the network of Pokémon they connect with. After another day of taking requests, Nuzleaf informs the Player that he will be gone for a couple days again and the Partner invites them to their house for dinner. When Nuzleaf returns a few days later, the Partner asks him to invite the Partner and Carracosta to dinner to repay the Partner's previous kindness,
Summer vacation starts for the school and the Player and Partner see Ampharos off as he leaves to explore a new area. While spending the summer completing requests, the Player and Partner meet with Pancham and Shelmet, who reveal there are rumors of the school being haunted at night, scaring the Player. That night Watchog investigates the school to disprove the rumors, but is attacked by an unknown being.
The Player and Partner learn Watchog was found unconscious after being scared by something he can't remember. That night, Audino and Farfetch'd watch the school to search for what made Watchog faint and Farfatch'd disappears. The following day, the Player and Partner learn of Farfetch'd's disappearance when Magnezone begins a search for him. Magneton arrives and reveals he has found a witness who says that Farfetch'd was seen being taken away by strange flames. The following day, Farfetch'd is found by the shore of the lake and he vague recalls some kind of ghostly encounter.
=== Chapter 8 Prove your Mettle ===
The next day, Pancham gathers all the students from class and proposes a dare that they all sneak into school at night to check the rumors of it being haunted. That night, everyone gathers at the school and eventually become surrounded by blue flames. A giant shadow appears and everyone passes out in fear. When they awaken, they discover that Shelmet, Espurr and Pancham are missing. Espurr returns and reveals that she was the only one not to pass out and saw Shelmet and Pancham were taken by the flames to a closed of area of the village, the Ancient Barrow. Despite being scared, the Partner rallies the class to overcome their fears and save Shelmet and Pancham.
When the group reaches the end of the dungeon, they find Shelmet and Pancham being held captive by a being called the "Dark Land Emissary." The Dark Land Emissary agrees to let the group go if they abandon Pancham and Shelmet, but the Partner refuses (despite being scared out of their wits) and battles the Dark Land Emissary, revealed to be a Giratina, and its Litwick henchmen with the group. After Giratina is defeated, it is revealed to actually be an illusion by a Solosis. The Litwick apologize for the trouble they caused and explain that they need to feed on the fear of others to feed themselves. In order to keep from being discovered and getting chased out of town, Solosis helped them scare others with its illusions so they could feed themselves. They beg the group not to tell anyone so they won't be kicked out of town and promise to cause less trouble. The Partner realizes the Litwick aren't malicious and agrees not to tell anyone if they stop pulling big scaring stunts and agree to do nice things to make up for the trouble the cause to others. Pancham and Shelmet are released and taken back to the village, but the Player and Partner are caught by their guardians.
=== Chapter 10 The Villager's Secret Spot ===
The next day, Nuzleaf asks the Player if any of their memories have returned yet, but the Player hasn't remember anything. When the Player goes to meet with the Partner, they overhear them being punished for sneaking out by cleaning and find a note from them apologizing for being unable to help explore that day. When they ask their classmates to help them explore for the day, they reveal they all came clean about sneaking out and one of them joins the Player for the day. When the Player returns for exploring and the Partner finishes their punishment, Nuzleaf suggests that they explore Revelation Mountain, a sacred place to the village, one day.
A Pelipper arrives the next day and drops off the news about Pokémon being turned to stone in other places. After finishing exploring for the day, the Partner asks Carracosta about Revelation Mountain and the latter reveals that even though Revelation Mountain is sacred and forbidden from being accessed, no one knows why.
The next day, Nuzleaf secretly tells the two that he is going to explore Revelation Mountain because he suspects that its secrets may be connected to the Player's amnesia and why they were turned into a Pokémon. The Player and Partner reluctantly agree to go along to see if they can find answers. Nuzleaf tricks the guard protecting the gate around Revelation Mountain, Hippopotas, into thinking there was a schedule change and sneaks past the gate with the Player and Partner. When the group reaches the next get, they find it is guarded by the police, a Beedrill, and a Poliwrath. Seeing that there is no way to get by the gate, the group cuts the exploration short and return to the village. That night, the Player decides to keep waiting to see if their memory returns, but worries about the Beheeyem finding them, so they decide to leave the village to keep everyone safe.
=== Chapter 10 A Journey Begins ===
The next day, the Player overhears that the Beheeyem have been spotted outside the village. After exploring for the day, the Player tells the Partner about their plans to leave to escape the Beheeyem and the Partner decides to come with them. Afterward, the Player tells Nuzleaf about their decision, but Nuzleaf insists they stay in the village where they are protected. The following day, the Player overhears the Partner arguing with Carracosta about leaving and the Partner takes the Player to speak with the other villagers, only for them to tell the two that leaving is too dangerous. Despite having their plan rejected, the Partner realizes they always wanted to leave the village to explore the world, but are stuck about what to do. 
After another day of exploring, the Partner reveals they plan to sneak out of the village even if the adults don't agree and join the Expedition Society. The Player agrees to sneak away with the Partner and agree to sneak out at night, but sense someone watching them. That night, the Player sneaks out and meets with the Partner, who asks them to take one last look at the village from the hilltop before they leave. After taking a leaving look of the village, the two prepare to leave, but are stopped by their classmates. Espurr admits that she overheard the two preparing to leave and gathered the class to see them off. The class also reveal they were given several letters from the villagers, including Nuzleaf and Carracosta, wishing the two luck in their journey. With the village's blessing, the two set off for Lively Town.
=== Chapter 11 Over the Mountains ===
The two reach the a mountain near lively town and after crossing it, arrive at a cave entrance where they rest for the night. While setting up camp, the Partner tells the Player more about the Expedition Society. The Pokémon Expedition Society conducts expeditions across the world to discover new places and Pokémon, storing all the information in the Pokémon Nexus, a system that can create a map of the world. Despite children not being allowed to join, the Partner is hopeful they will still be excepted.
The next day, the two travel through the cave and finally reach Lively Town. While searching for the Expedition Society's building, the pair run into a Krokorok that tries to mug them, but is repeatedly trampled by a group of Pokémon chasing after a Swirlix and gives up. Though confused by the incident, the pair continue their search and find the Expedition Society building. They search the building, only to find it empty. While searching the building, they find the Pokémon Nexus and the group of Pokémon from earlier arrive, continuing to chase Swirlix because he ate all their food. A Dedenne from the group launches an attack at Swirlix in anger, but ends up destroying the Pokémon Nexus and the group (including Swirlix) collapse from hunger. The group explains they are the Expedition Society and the pair bring them some food from the town plaza. After sharing a meal with the Expedition Society, the Partner explains they and the Player want to join. The Expedition Society reluctantly explains that they can't let them join because children aren't allow, but Ampharos, who is revealed to be the chief of the Expedition Society, arrives with another member, Mawile, and allows the two to join, removing the rule preventing them from joining (even though he was the one who made it). 
The pair are formally accepted into the Expedition Society and are introduced to its members: Buizel, the underwater explorer, Archen, who explores the skies, Dedenne, who is in charge of communication through signals she sends through her whiskers, Bunnelby, the underground explorer, Swirlix, the steward of the Expedition Society (though her gluttony causes her to constantly eat all the food), Mawile, the Society's archeologist, and Ampharos, chief of the Expedition Society. Dedenne explains there is one more member on the Expedition Society, but they are currently sleeping so the two will have to wait to meet them. Ampharos explains that he said he didn't work for the Expedition Society because he led it and the Player and Partner are shown to their room for the night.
=== Chapter 12 Life at the Expedition Society ===
The next morning, the Player and Partner attend a meeting of the Expedition Society to discuss the destroyed Nexus (which Ampharos mentions has been destroyed many times previous due to the Society's antics). Ampharos decides to have Jirachi, the final member of the Expedition Society, repair the Nexus and continue filling out the map once it is fixed. The Player and Partner are given an official exploration bag and Ampharos explains that their junior badges were actually real badges all along. Afterward, Ampharos asks the pair to wake up Jirachi, warning it is a harder task than it sounds.
When the Player and Partner find Jirachi in the base's observatory, Jirachi sleepily warns that he won't fully wake up easily and that he tends to inadvertently attack those around him while tossing and turning in his sleep. After Jirachi is battled and defeated, he fully wakes up with no memory of the battle and introduces himself as the Expedition Society's astronomer. Jirachi begins repairing the Nexus and the Player and Partner are assigned to continue exploring and helping other Pokémon. After finishing work for the day, the Expedition Society has dinner before heading to bed.
The following day, Jirachi finishes restoring the Nexus, but was unable to restore the data, meaning the society will have to start over from nearly nothing. The Player and Partner are assigned to start gathering data on the places that have been previously mapped and are given a new expedition gadget that allows them to communicate with Dedenne, display the map from the Nexus, and raise their expedition rank
After a few days of exploring, Krokorok tries to mug the pair again, but Buizel arrives and warns him to leave the two alone. Krokorok's boss, Krookodile, arrives and threatens the three before storming off with Krokorok. Buizel warns the pair to avoid Krookodile and they resume their explorations. During dinner, the two learn that Archen explores other continent via the Lapras Travel Liner and are invited by him to explore with him the next day.
=== Chapter 13 Across the Sea ===
The next day, the Player, Partner, and Archen travel to Lapras' Travel Liner where Lapras explains they will need to buy different passes to travel to different continents. Archen (under pressure) buys the two a pass. 
Meanwhile, a Latios and Latias flee from some unknown danger and try to reach Time Travel Lake.
When the Player, Partner, and Archen arrive at their destination, they discover that Archen accidentally bought a pass to Baram Town on the Air Continent instead of their intended destination. While looking around, the three overhear some Pokémon discussing the incidents where Pokémon are turning to stone on the Air Continent and the rumor that it is being done by a being called the "Flaming Phantom." They explain the Flaming Phantom has been spotted near Mystical Forest and is believed to be trying to find Time Travel Lake, which lies at the center of it, to find Celebi, a Pokémon that inhabits the lake. Suddenly, two objects crash into Mystical Forest and Archen decides to investigate with the Player and Partner insisting they go with they go along with him.
When the three travel to the end of dungeon, they find one of the crashed objects was Latios turned to stone. The Player and Partner go ahead to look for clues while Archen inspects the stone Latios, wondering why he traveled all the way to Mystical Forest and who turned him to stone. While searching, the Player and Partner find Latias turned to stone and the Flaming Phantom, an Entei, appears and accuses them of being responsible for turning Pokémon to stone. Before Entei can attack, Archen arrives and explains that he and the pair are members of the Expedition Society. Realizing that Celebi is not in the forest, Entei leaves after warning the three not to get in his way. The three return to the Expedition Society base and the Player and Partner head to bed, awed by the amazingness of the Expedition Society. Archen explains the day's events to the Expedition and everyone decides to continue their work until more clues appear. Ampharos goes off to eat Swirlix's stash of leftovers (much to the latter's dismay) and makes a decision about Entei.
At dinner the next day, Dedenne announces the Expedition Society will partake in an outing in two days.
=== Chapter 14 A Fun Outing ===
On the day of the outing, Ampharos announces Dedeene and Jirachi will stay behind because of their duties and the rest of the Expedition Society head off for the outing on Lapras. They arrive at their destination, Fire Island, and Ampharos explains everyone will split into teams and meet at the island's volcanic peak. The Player and Partner are teamed up with Buizel and the three begin their journey up the island. 
When the three near the summit, they are ambushed by a Magmortar and a group of Magmar. After the enemies are defeated, the Partner questions Buizel on the unexpected difficulty of the outing, but Buizel explains that he doesn't know the details and urges them to keep going. The trio reach the summit and discover they are the first team to make reach it. Entei appears, angered at the three's presence, and Buizel steps in to protect the Player and Partner, but is quickly defeated. Before Entei can finish Buizel off, the Player and Partner battle Entei to save him.
The Player and Partner are overwhelmed by Entei's might, but before Entei can finish them, the pair's Harmony Scarves react to some unknown power and evolve them to their final forms. The pair battle Entei again and with their new strength, defeat him. After Entei is defeated, the pair return to their original forms, but Entei gets up and prepares to attack again, only to be stopped by Ampharos and Mawhile. Ampharos explains that the Expedition Soceity came to Fire Island because they needed to know if Entei was responsible for turning Pokémon to stone, but those suspicions have been disproven. He apologizes for intruding on Entei's territory and promises the Expedition Society will leave. Entei leaves after explaining he took action because he sensed danger was approaching and Mawhile explains to the Player and Partner that they temporarily evolved, but the circumstances were different than usual and are linked to their scarves. The rest of the Expedition Society reaches the summit and are informed about what transpired at the summit. After eating lunch to regain their strength, the Expedition Society returns to their base. As the Partner wonders what the secret of their Harmony Scarves is, a dark power begins spreading across a strange tree in an unknown land.
A few days later, Lively Town is subjected to a hot day, one of several that have been happening lately. Jirachi observes the sun from the Expedition Society's observatory and determines the sun is getting closer but is interrupted by a visit from Nuzleaf. Nuzleaf explains he wanted to check up on the Player and Partner while on some business near Lively Town and the pair return in time to meet him. Nuzleaf is informed that the pair have officially joined the Expedition Society and he lets the Player know he understands why they snuck away. He also reveals the Beheeyem never showed up inside the village and Jirachi, after learning about the Player's transformation into a Pokémon, decides to inform the rest of the Expedition Society so they can help protect the Player. Nuzleaf returns to Serene Village and that night, the Expedition Society learns about the Player's secret, but they remain calm and promise to help protect the Player.
After another day of requests, the Player overhears Pokémon discussing the abnormal heat and the incidents where Pokémon have been turned to stone and wonders what is happening. Meanwhile, multiple legendary Pokémon learn of the stone incidents where even legendary and mythical Pokémon are being target, and wonder who is responsible for it.
The next day, Ampharos reveals that someone has been giving threats to the Pokémon that were turned to stone and is targeting legendary Pokémon. Ampharos tells the Player and Partner the Expedition Society has been investigating the crisis to protect the world and assigns more members to the investigation. The Player and Partner are assigned to investigate Lively Town for information for the next few days.
=== Chapter 15 A New Warning ===
After a few days, several papers are found in Lively Town declaring the next Pokémon to be turned to stone will be Entei on Showdown Mountain. Knowing Entei will go to Showdown Mountain, Ampharos decides he, Mawile, Archen, Buizel, and Bunnelby will go investigate. The Partner, having seen the danger the world is in, begs Ampharos to let them and the Player go and, with Archen's support, are allowed to join the investigation. The pair are teamed up with Mawile and Archen and the Expedition Society sets out for Showdown Mountain.
Once the Player's group nears the summit of Showdown Mountain, Mawile spots Krookodile following them, but he drops something and flees when spotted. Mawile picks up the tablet Krookodile dropped, and the group continues heading up the mountain. The group reaches the summit, but discovers Entei has already been turned to stone. Mawile relays what they discovered to Dedenne and Ampharos's group arrives and decides everyone should return home. At the Expedition Society base, Ampharos is informed about Krookodile being sighted on Showdown Mountain and the stone tablet he left behind. Mawile decides to study the tablet and Buizel and Archen are assigned to search for Krookodile.
At dinner, Buizel and Archen report that Krookodile is nowhere to be found and while searching his home, they found a half-written threat letter about turning Pokémon to stone. Mawhile also reveals that she has deciphered the writing on the stone tablet and it describes a previous time where Pokémon were being turned to stone. She determines more details hidden in the Prehistoric Ruins at the east that could provide hints and possibly a way to bring Pokémon back from stone.
The next day, Ampharos prepares to start the expedition to the Prehistoric Ruins, but Dedenee arrives with news that Krookodile has been seen heading for Serene Village. Ampharos decides to split everyone into two groups, one to go after Krookodile and another to investigate the ruins. The Player and Partner are assigned to go after Krookodile since they are familiar with Serene Village and Archen is picked to go with them.
=== Chapter 16 The Sealed Spring ===
When the trio reach Serene Village, they discover everything is normal and meet with Espurr again. The Partner asks Espurr if she has seen Krookodile, but Espurr tells them that he hasn't been seen in the village. Suddenly, Nuzleaf arrives and reveals he saw Krookodile invading Revelation Mountain. Archen asks Nuzleaf to take them to where he saw Krookodile, but the Partner has Espurr stay behind to contact Ampharos with her telepathy in case something goes wrong. When the group leaves for Revelation Mountain, Espurr quietly follows them. Nuzleaf shows the Player, Partner, and Archen the destroyed gate and Archen guesses that Krookodile is after whatever is at the top of Revelation Mountain.
When the four reach the second gate, they discover its guards have been knocked out and the gate broken through by Krookodile. On the way to the summit, the group receives a message with their Expedition Gadgets from Dedenee and the team exploring the Prehistoric Ruins, but it interrupted when the team is attacked by unknown assailants. Despite worrying about the others, the group is forced to keep going to find Krookodile.
When the group reaches the summit, where they find a spring protected by a barrier. Nuzleaf finds a stone tablet next to the spring covered in ancient writing and the Partner is somehow able to read it. The tablet says that only a human can break the barrier to overcome a crisis. Nuzleaf determines that someone foresaw some kind of crisis and summoned the Player to break the barrier. Suddenly, the group receives another message from the other team who explain that the Pokémon who attacked them were the guardians of the ruins and stopped attacking once they knew the ruins weren't in danger. Dedenee reveals that the ruins revealed a way to bring Pokémon back from stone, a special water called Luminous Water can reverse the effect, and that water is sealed away on Revelation Mountain. The group realizes that the spring is the Luminous Water and everyone convinces the Player to try and break the Barrier. However, Krookodile appears and begins stomping toward the group. Before anything can happen, a Raikou and Suicune appear to avenge Entei. Nuzleaf urges the Player to break the barrier while Krookodile is distracted, but Krookodile makes his way toward the group. The Player senses something is wrong when Krookodile mentions a deal with money, but is pressured into unsealing the spring by touching the barrier. 
When the spring is unsealed, the Partner gloats to Krookodile that he can't turn them to stone anymore. However, Krookodile has no idea what the spring water is and reveals he came to collect money for being hired to drop the warnings and traveling to Revelation Mountain by Nuzleaf. Nuzleaf's attitude suddenly turns sinister and he rejoices over the barrier being broken before turning Krookodile to stone with a dark power. Nuzleaf reveals he was behind Pokémon turning to stone, but everyone prepares to fight him while Archen orders the Player to get the Luminous Water. However, a Yveltal appears and turns everyone to stone with the same dark power as Nuzleaf.
In the Prehistoric Ruins, the team loses connection with the Player's team, but are ambushed by the ruin guardians, who are actually the Beheeyem that attacked the Player, and turned to stone with dark power.
Back at Revelation Mountain, Nuzleaf assumes the Beheeyem have finished their mission and celebrates obtaining the Luminous Water with Yveltal. A massive darkness spreads across the world which Yveltal uses to relay a message. He declares himself the destroyer of all Pokémon and that he plans hunt all other Pokémon across the world and send them to the "void" to steal their strength. Nuzleaf and Yveltal begin a series of attack to turn Pokémon to stone all across the world.
A few days later, Ampharos and Jirachi discover the Luminous Water is gone and learn that the rest of the Expedition Society has been turned to stone. Espurr meets up with them, having joined forces, and reports that everyone in Serene Village has been turned to stone. Ampharos promises to save everyone and foresees a chance will come.
=== Chapter 17 The Voidlands ===
The Player and Partner awaken in a dark dimension and remember what happened to them. The Partner guesses that the dimension is where Pokémon go when they are turned to stone and wonders why Nuzleaf is turning Pokémon to stone. Though scared and confused, the two vow to find answers and begin traversing the strange dimension. After traveling for a bit, the pair receive a communication from Dedenee which they use to reunite with her and Mawile.
Dedenee reveals how the ruins team got turned to stone and the Player and Partner realize the Beheeyem are in league with Nuzleaf. Mawile explains they are in the Voidlands, the place the spirits of Pokémon go where they are turned to stone. She reveals she found writing on the wall which describes the Voidlands and the Partner reveals they can read the ancient writing, something even Mawile is unable to do easily, and discovers a passage stating the enemy Pokémon in the Voidlands are actually apparitions of hate given form. Mawile determines the writing was left behind by Pokémon who were turned to stone long ago and that they may have left clues on how to escape the Voidlands. The Partner vows to find the rest of the Expedition Society and escape the Voidlands.
After traveling through a cave, the group finds more writing and the Partner reads it. The writing reveals a being known as Dark Matter is responsible for turning Pokémon to stone, and absorbs the energy of those turned to stone to grow stronger. A second section of writing warns of beings called Void Shadows, but is cut off before it could elaborate. Dedenne suddenly picks up Buizel, Archen, and Bunnelby, and guides them to reunite with the group. With everyone reunited, they rally to escape the Voidlands, unaware a black mass is watching them.
=== Chapter 18 Hope ===
The group follows the only path forward until they find another wall with writing that the Partner reads. The writing reveals that Dark Matter has possessed something called the Tree of Life and is stealing away its strength, which will eventually destroy it. Mawile explains the Tree of Life is a giant tree that is the source of life and gives the world vitality. If the Tree of Life is threatened, world itself will be in danger. While everyone tries to think about what to do, they notice Buizel and Bunnelby are missing. When the find Buizel, Bunnelby arrives and warns that it is actually an imposter. Mawile attacks Bunnelby, revealing he is also an imposter, and the imposters transform into their real forms, black masses of shadows. More shadows surround them and Mawile guesses that Buizel and Bunnelby have been captured before fighting the shadows. 
After the Void Shadows are defeated, more appear and threaten to overwhelm the group. Dedenee and Archen are captured by the Void Shadows and the Player is also caught by one of the Void Shadows. Fortunately, Entei, Raikou and Suicune arrive and blast away the Void Shadows, saving the Player. Everyone flees to safety and the legendary beasts declare they plan to use the Player, Partner, and Mawile to aid their escape since the Player is human and may be the key to escaping, Mawile can read the writings, and the Player and Partner's Harmony Scarves have strange powers. They make it clear that the three owe them for saving them from the Void Shadows and that are willing to sacrifice them to escape. Entei reveals he has deciphered some of the writings that reveal that there is a place called Reverse Mountain that is linked to the real world and is the key to returning. Though the Partner is concerned about leaving the capture Expedition Society members behind, Mawile explains that the best thing they can do is escape and find a way to bring them back from the real world.
The group climbs Reverse Mountain and when they get close to the summit, the discover more writing which reveals that there is an exit back to the real world, but it is guard by many Void Shadows. It also reveals that Dark Matter is connected to astrological bodies and if it destroyed, the world can be saved and all those turned to stone will revert to normal. Mawile determines Dark Matter goes through periods of activity and rest depending on the position of the stars and that it has been defeated before. The Pokémon of the past have prepared for Dark Matter's return and set up countermeasures such as the Luminous Water. 
The Legendary Beasts order everyone to keep moving and the group soon reaches the summit. There, several Void Shadows drop down from a black mass in the sky which the Legendary Beasts destroy. When the shadows are destroyed, a ray of light shoots down from the black mass and briefly opens a gate before closing after more Void Shadows arrive. Realizing the beam of light is the exit and that it can only appear when the Void Shadows are destroyed, the group battles the shadows which take the form of different Pokémon. After the Void Shadows are destroyed, the gate appears, but more shadows keep appearing and block the way long enough for it to close. Everyone becomes exhausted from the battles and Entei asks Mawile for a favor. The Legendary Beasts blast away the shadows again and Mawile throws the Player and Partner past the shadows and in front of the gate. The Legendary Beasts reveal that they knew the Player and Partner had the best chance of saving the world and that they planned to get them back to the real world at all costs from the start. The Player and Partner jumped through the gate just before it closes while Mawile and the Legendary Beasts stay behind to fight the Shadows.
The Player and Partner awaken in the real world and discover the Luminous Water is gone. Though saddened that they were the only ones to escape the Player urges the Partner to move on and save the world. The Partner wonders why everyone chose to put their faith in them and the Player, but is forced to put their questions aside and the two set out to find Ampharos. The two return to Lively Town, but discover everyone is gone and though worried about their friends, reluctantly move on and go to Lively Town. 
=== Chapter 19 This Planet is Already... ===
When the two reach Lively Town, the discover many of its residents, including Swirlix, have been turned to stone. They head to the Expedition Society building where they discover the shopkeepers, Jirachi, and Ampharos are okay. The shopkeepers reveal Yveltal's message to the world and the attacks he's carried out. When the two go searching for Ampharos and Jirachi, they find Espurr, who joyfully reunites with them. Espurr reveals that Ampharos and Jirachu are out searching for clues and that she has been using her Telepathy to help them keep in touch, but also sadly reveals everyone in Serene Village was turned to stone. The Partner runs off in grief, but the Player knows that they will be able to overcome it for the sake of saving the world. Suddenly, the Player and Espurr hear someone sneak into the observatory and discover it is one of the Beheeyem and attack it. 
While battling the Beheeyem, the Partner returns and helps defeat it. Beheeyem explains that he was actually trying to get away from Nuzleaf and Yveltal, and that they were all being controlled by Dark Matter as pawns. When the Player and Partner escaped from the Voidlands, it created a shock to those under Dark Matter's control and allowed Beheeyem to free itself. Beheeyem fled when it had the chance and Espurr, recalling that Ampharos told her that Dark Matter can control Pokémon with any darkness in their hearts and grant them its dark powers, choses to believe it. Beheeyem explains that it no longer has the dark power to turn others to stone because it was freed from Dark Matter's influence and that it came to reveal the location of both Dark Matter and the Tree of Life. It reveals the Tree of Life is deep inside the Prehistoric Ruins, far deeper than the Expedition Society reached and came to find someone who could destroy Dark Matter. The Partner has Espurr try to contact Ampharos, but she fails to reach him and the Partner reluctantly decides to trust Beheeyem and go with him to the Prehistoric Ruins. Though suspicious of Beheeyem, the Player and Partner set out for the Prehistoric Ruins with it. 
After the Player and Partner set out, Espurr gets in contact Nuzleaf and is revealed to be working with him. 
=== Chapter 20 The Prehistoric Ruins to the East ===
The Player, Partner, and Beheeyem arrive at the island where the Prehistoric Ruins are and make their way through a submerged cave to reach the ruins. When they reach the ruins entrance, the Partner asks Beheeyem if it remembers what it did under Dark Matter's control. After Beheeyem answers that it does remember, the Partner asks why Nuzleaf tricked the Player, still suspecting a trap, Beheeyem reveals it was because of who that Player is and what they could have remembered but doesn't say anything else about the subject. 
While traversing the dungeon, the three discover the stone bodies of the Expedition Society members who previously went to the ruins, but Beheeyem urges them to keep moving. When the three reach the end of the ruins, all they find is an empty chamber to Beheeyem's confusion. Beheeyem realizes the chamber is actually a trap set up for all three of them, explaining Nuzleaf told them the location of the Tree of Life after he broke free of Dark Matter's control to lure them all there after suspecting they would betray him. Nuzleaf and the other two Beheeyem appear and Nuzleaf reveals the Player knew who they were when they first arrived in the Pokémon world until he had the Beheeyem wipe the their memories. They then decided to use the Player's amnesia to their advantage and trick them into breaking the barrier on the Luminous Water and so they could use it to make them stronger, which was set up by an ancient Pokémon who was responsible for the Player being summoned. Nuzleaf then reveals that the chamber they are currently in will send anyone turned to stone to the deepest part of the Voidlands where escape is impossible and that Espurr is allied with him. Espurr arrives and reveals that she was found when the Player and Partner were turned to stone and forced to help Nuzleaf to escape the same fate by being a spy. Nuzleaf offers the Beheeyem that betrayed him to return to his side and it reluctantly agrees to avoid being turned to stone. Nuzleaf prepares to turn the Player and Partner to stone, but is stopped by Ampharos, who arrives with Jirachi and Celebi. Celebi teleports everyone, including Espurr away to safety. 
Everyone arrives in a forest, which Celebi explains is on an island in the south and far away from the ruins. Ampharos introduces Celebi as a friend of his who has been helping him investigate the crisis with his ability to time travel. Celebi explains that Entei originally asked him to investigate Pokémon being turned to stone and Jirachi reveals that if the Tree of Life is withered away by Dark Matter, the planet will stop spinning and be drawn into the sun, something that has already been happening and causing the heat waves. Ampharos then explains that Espurr was actually a double agent and she set up the rescue from the ruins. He then prepares to tell the Player and Partner everything he learned through his investigations. 
=== Chapter 21 Dark Matter ===
Ampharos explains that Dark Matter is an amalgamation of negative emotions from all Pokémon in the world. Since it is fueled by the emotions of all Pokémon, the Partner wonders if it can be destroyed and Ampharos reveals that Dark Matter was previously subdued by the alignment of the stars, but can never be fully defeated. Celebi reveals that he saw the past where not only Pokémon who fought against Dark Matter, but also a human, which he suspects to be the Player. The human was able to fight against Dark Matter long enough for the stars to subdue it, and knowing it would eventually return, helped the Pokémon of the past set up countermeasures such as the Luminous Water and the Harmony Scarves. The scarves were made by an ancient Pokémon called Mew, who led the battle against Dark Matter, using materials from the Tree of Life. and passed down to the Partner for unknown reasons. Ampharos explains that is most likely that it was Mew who summoned the Player and Celebi reveals the scarves are the key to defeating Dark Matter. Ampharos then reveals that they are currently in Primeval Forest, which leads to the Tree of Life, and Jirachi urges everyone to get moving.
When the group reaches Primeval Forest, they find the Tree of Life. but it is already wilting because of Dark Matter. Before the group can start climbing the tree, Nuzleaf, the Beheeyem, and Yveltal appear, but Dark Matter's control over them is growing stronger and stripping away their sense of self. The Beheeyem who is freed from Dark Matter's control begs Nuzleaf and the others to stop, unable to bear watching them commit anymore evil acts, but is turned to stone by them. When they try to the group to stone, the Harmony Scarves react to the Tree of Life, protecting them and evolving them again. Ampharos realizes the scarves resonate with the Tree of Life's power, and since Fire Island was close to Primeval Forest, it is why they evolved during the battle with Entei. Celebi explains the power of the Tree of Life is protecting them from turning to stone and that the Tree of Life is still alive. The group battles against Nuzleaf's group and emerges victorious. 
After being defeated, Nuzleaf and the others are freed from Dark Matter's control, but suddenly disappear and a sinister laughter fills the air. The group realize the voice is Dark Matter's and the Tree of Life is lifted out of the ground and pulled into the sky. The Player and Partner revert to normal, and Celebi is unable to teleport anyone to the Tree because of Dark Matter's power. The Partner makes a desperate dash for the tree, climbing the falling rubble and being lifted up by the others, but fails to reach the Tree of Life in time. Ampharos break's the Partner's fall and Jirachi and Celebi try to catch up the tree, but it is pulled away too fast for them to reach. and Dark Matter declares tha without the Tree of Life, the world will be pulled into the sun and that it shall return the world to the void. It gloats that the negative feelings of Pokémon brought it to life and they are responsible for their own destruction. However, when all seems lost, the group hears a roar and discovers something is stopping the Tree of Life from being pulled away further. Deoxys and Rayquaza are working together to push the tree down and everyone hears the voice of the legendary Pokémon Arceus. Arceus, reveals the Pokémon of the world are working together to hold the Tree of Life, by using the powers of a Mewtwo to hold it back and various flying Pokémon to further slow its ascent. However, Dark Matter's power is keeping anyone from confronting Dark Matter and Acreus explains that only the Player and Partner, who wear the Harmony Scarves, can resist it. Espurr reveals that Ampharos and Jirachi have been gathering allies and preparing for the this moment while the Player and Partner were in the Voidlands. Arceus transports the Player and Partner to the Tree of Life to confront Dark Matter.
=== Chapter 22 Battle in the Stratosphere ===
When the Player and Partner are transported to the Tree of Life, they discover that the air is thin since it has been pulled into the Stratosphere. Fortunately, their scarves evolve them again and give them the strength needed to climb the tree. Arceus warns the two that the Tree of Life is still ascending, Dark Matter continues to decaying the tree, and that it will try to stop them with dark illusion of Pokémon. 
As the pair climb up the tree, they find Nuzleaf, Yveltal, the two Beheeyem restrained by Dark Matter's power and free Nuzleaf and the Beheeyem first. The freed Pokémon flee in remorse for their actions under Dark Matter's influence. When Yveltal is freed, he wonders why the two saved him after what he did before disappearing. The pair keep moving up the tree and finally find Dark Matter, who transforms the area into world of its own making. The two discover the Tree of Life still has strength and battle Dark Matter, managing to damage it. Before the pair can destroy Dark Matter, the Tree of Life runs out of energy and withers. Dark Matter creates a protective shell around itself and the Player and Partner revert to their normal forms as Dark Matter turns the Pokémon trying to stop the Tree of Life to stone. However, when Dark Matter boasts of its victory, Yveltal, Nuzleaf, and the two Beheeyem appear and attack Dark Matter to make amends for what they did under its control. Dark Matter turns them the stone as well and claims that the Player and Partner have lost their strength and their allies, but the Partner refuses to give up and it inspires the Player to keep fighting against Dark Matter. The Player repeatedly attacks Dark Matter, despite its attempts to make them give up, and hears the voices of those turned to stone encouraging them to keep fighting. Realizing those who were turned to stone are still with them in spirit and the many Pokémon still remaining are with them as well, the Player and Partner continue attacking Dark Matter. The manage to destroy its shell and severly damage its core, but before the Player can destroy it, Dark Matter reveals it will only appear again in a future generation. However, the Partner is undeterred and explains the negative parts of everyone are an essential part of them and accepts Dark Matter's existence before destroying it. When Dark Matter is destroyed, those turned to stone are restored and the Tree of Life returns to normal.
=== Final Chapter An End to Beginnings ===
The Player and Partner awaken in Primeval Forest and discover the restored Tree of Life. An orb of light emerges from the tree and lands in front of the two, taking the form of Xerneas. Xerneas introduces itself as the embodiment of the Tree of Life and reveals that Dark Matter is gone forever and that the world has stopped being pulled toward the sun. Jirachi comes crashing in (literally) with Celebi in tow and Xerneas explains that Arceus sent a message across the world telling everyone what happened. Ampharos and Espurr arrive (with Ampharos accidently body slamming the Partner trying to hug them and nearly doing the same to the Player) and everyone receives a message from Dedenee, who reveals those turned to stone have been restored. Everyone returns to Lively Town where they reunite with those turned to stone and celebrate the world being saved. 
A few days later, the Player and Partner take Espurr back to Serene Village to visit. On the way back, the Player begins to worry that since Dark Matter is defeat and the reason they were summoned back is fulfilled, they will be sent back to the human world. When the three return to Serene Village, the discover the village is still empty at first, but discover Espurr was just planning a surprise with her telepathy and all the villagers come out to great them. Carracosta reveals that Nuzleaf returned to the village and apologized for what he did under Dark Matter's control, but he left, unable to face the Player for what he did to them yet. Principal Simipour assures them that Nuzleaf was sincere and everyone understands he wasn't responsible for his actions and has been forgiven. Everyone celebrates the world being saved and throws a party where the Partner recounts their adventures. That night, the Player wonders what they will do if they are sent back to the human world, but decides that they want to stay in the Pokémon world and will find a way to do so.
The next day, the Player meets with the Partner at the village hilltop and reminisce. The Player tells the Partner about how they might be sent back to the human world, but Froakie reveals that he was contacted by Xerneas and remembered that he was Mew in a previous life. Mew and the Player worked together to defeat Dark Matter, but they knew Dark Matter would return and Mew sent its spirit to the future where they were reborn as the Partner and that it was actually Mew who took the Player's memories in an agreement they made before the Player came to the Pokémon world. Despite setting up countermeasures like the Luminous Water, Mew knew that things would only repeat if they relied on what they already knew, so they had the Player's memories erased. The Partner then reveals that when they accepted Dark Matter and caused it to disappear, the park of Dark Matter that came from Mew also disappeared, which would lead the Partner's eventually destruction. The Partner begins to fade away explains they wanted to tell the Player everything before the disappeared and had Xerneas keep them around until they could speak with the Player. The Partner says their goodbyes to the Player and gives some parting words of encouragement before disappearing in a orb of light.
As the Player cries over the loss of the Partner, the credits roll, ending the main game.
=== Post-Game ===
Sometime after Dark Matter's destruction and the Partner's disappearance, the Pokémon world thrives in peace and the Player stays in the world and continues being a part of the Expedition Society, though they still mourn the Partner's loss. After another day of exploring, Ampharos consoles the Player and tells them there is the possibility of bringing the Partner back. He tells them of a Pokémon called Xatu, who lives on the Sand Continent and can see the past and future, and encourages them to speak with him.
When the Player finds Xatu, the latter inspects the former's Harmony Scarf and reveals Mew, the Partner's previous incarnation, is within Mystery Jungle. The Player decides to find Mew in hopes of finding a way to bring the Partner back. After the Player leaves, Xatu senses another visitor is hiding nearby. 
The next day, the Player travels to Mystery Jungle and finds Mew at the end. The Player discovers Mew has no memories of the Player or the Partner, but they end up following the Player home. Mew is offered a temporary spot in the Expedition Society by Ampharos so the Player has some help during exploration. That night, the Player contemplate Mew being different than the Partner and the past life where they fought Dark Matter, but decides to let Mew adventure with them.
After a few days of exploring with Mew, the Player awakens to discover they are on the hilltop in Serene Village with no memory to as how they got there. While heading back through the village, the Player recalls a memory where Mew kept falling ill and they return to Lively Town to check on them. When they return to their room in the Expedition Society base, they discover that Mew is gone and remembers more of what happened. Xatu came to investigate Mew's illness and determined it was the influence of Dark Matter that was the source, because a part of it remains inside Mew. During a time when Mew was feeling better, the Player took them to Serene Village, but they can't remember anything beyond that point. Ampharos and Mawile arrive and reveal they received a letter stating that Mew's kidnappers are playing to destroy Mew in Purifying Cave so Dark Matter can never return. Mawile explains that Purifying Cave holds a mysterious power that can be used to destroy Mew. Ampharos refuses to allow the kidnapper's plan and orders the Player to go to Purifying Cave while he gathers the Expedition Society and follow them.
The Player travels to Purifying Cave and when they reach the end, they discover Mew unconscious and that Nuzleaf and the Beheeyem are the kidnappers. Nuzleaf apologizes for what he is going to do, but declares that Dark Matter must never come back and that they can't bear the thought of going through their ordeal again. Mew begins to fade away in light, but the Player refuses to let Mew disappear like the Partner did, even if it means fighting Dark Matter again. Suddenly, the Player's Harmony Scarf turns into light that merges with a similar light coming from Mew and restores the Partner. Mew awakens and explains they heard the Player's wish to stay with the Partner and Ampharos, Mawile, and Xatu arrive. They reveal that the entire kidnapping was a trick to bring the Player to the cave and Xatu reveals Mew's illness was actually caused by the Partner's existence inside them. They brought the Player to the cave so they could test their bond with the Partner and see if their feelings were strong enough to restore the Partner, the Nuzleaf and Beheeyem offered their help to atone for their actions under Dark Matter (though Mew reveals that he actually beat them up when they tried to stage the kidnapping so they had to bring them in on the plan). The Partner regains consciousness and reunites with the Player. Afterward, Mew returned to Mystery Jungle, though he remains an ally, Nuzleaf and the Beheeyem were accepted back into Serene Village, and the Player and Partner continue their explorations as a part of the Expedition Society. 
Sometime later, Ampharos reveals to the Player and Partner the existence of the Treasure Collection, a series of rare treasures scattered across the world, and challenges them to find them all.
==Characters==
*Player
*Partner
*Nuzleaf
*Beheeyem
*Deerling
*Pancham
*Shelmet
*Goomy
*Espurr
*Watchog
*Simipour
*Ampharos
*Buizel
*Archen
*Swirlix
*Dedenne
*Bunnelby
*Mawile
*Jirachi
*Entei
*Krookodile
*Suicune
*Raikou
*Yveltal
*Dark Matter
*Xerneas 
== Cameo Characters==
*Alakazam, Leader of Team A.C.T
*Charizard. Team A.C.T
*Tyranitar, Team A.C.T
*Whiscash, the elder of Whiscash Pond in Red and Blue rescue team
*Caterpie, the first rescued Pokémon in Red and Blue rescue team
*Butterfree, Caterpie's mother in Red and Blue rescue team
*Persian, ran Felicity Bank in Red/Blue Rescue Team
*Makuhita, ran the Makuhita Dojo in Red/Blue Rescue Team
*Gulpin, ran the Gulpin Link Shop in Red/Blue Rescue Team
*Gengar, formerly human turned into a Pokémon by Ninetales in Red and Blue rescue team. Formerly lead Team Meanies until he disbanded the team and disappeared after the resurrection of Gardevoir
*Ninetales, turned a selfish human (Gengar) into a Pokémon, creating its own legend in Red and Blue rescue team
*Absol, joined the player character's party to find Ninetales in Red/Blue Rescue Team
*Granbull, resident of Pokémon Square in Red/Blue Rescue Team, formerly Snubbull
*Lopunny, leader of Team Charm in Explorers of Time, Darkness and Sky
*Medicham, Team Charm in Explorers of Time, Darkness and Sky
*Gardevoir, Team Charm in Explorers of Time, Darkness and Sky
*Wigglytuff, leader of the Wigglytuff's Guild in Explorers of Time, Darkness and Sky
*Armaldo, a former outlaw and master of Wigglytuff as Igglybuff in Explorers of Sky
*Chatot, second-in-command in Wigglytuff's Guild in Explorers of Time, Darkness and Sky.
*Corphish, member of the Wigglytuff guild in Explorers of Time, Darkness and Sky.
*Bidoof, member of the Wigglytuff guild in Explorers of Time, Darkness and Sky.
*Snover, leader of Team Rogue in Explorers of Sky
*Bagon, member of Team Rogue in Explorers of Sky
*Gligar, member Team Rogue in Explorers of Sky
*Sunflora, member of the Wigglytuff guild in explorers of Time, Darkness and Sky
*Chimecho, member of the Wigglytuff guild in Explorers of Time, Darkness and Sky.
*Loudred, member of the Wigglytuff guild in Explorers of Time, Darkness and Sky, ran Sentry Duty with Diglett
*Diglett, member of the Wigglytuff guild in Explorers of Time, Darkness and Sky, ran Sentry Duty with Loudred
*Dugtrio, member of the Wigglytuff guild in Explorers of Time, Darkness, and Sky, Diglett's father
*Grovyle, collector of the time gears in Explorers of Darkness/Time/Sky
*Dusknoir, former servant of Primal Dialga in Explorers of Darkness/Time/Sky
*Sableye, Dusknoir's servant in Explorers of Darkness/Time/Sky
*Shiny Celebi, minor character in Explorers of Darkness/Time/Sky
*Weavile, Leader of Team AWD in Explorers of Darkness/Time/Sky
*Arbok and Drapion, Team AWD in Explorers of Darkness/Time/Sky
*Gallade, Roserade, and Rhyperior, Team Raider of Darkness/Time/Sky
*Duskull, ran Duskull Bank in Explorers of Darkness/Time/Sky
*Electivire, ran the Electivire Link Shop in Explorers of Darkness/Time/Sky
*Marowak, ran the Marowak Dojo in Explorers of Darkness/Time/Sky
*Skuntank, leader of Team Skull in Explorers of Darkness/Time/Sky
*Koffing and Zubat, Team Skull in Explorers of Darkness/Time/Sky
*Magnezone, the Police Chief in Explorers of Darkness/Time/Sky
*Emolga, an explorer of Magnagates in Gates to Infinity
*Dunsparce, an explorer the Magnagates in Gates to Infinity
*Hydreigon, Voice of Life in Gates to Infinity
*Umbreon, a Magnagate adventurer with his partner Espeon in Gates to Infinity
*Espeon, a Magnagate adventurer with her partner Umbreon in Gates to Infinity
*Virizion, a character in Gates to Infinity
*Keldeo, a Magnagate adventurer and Virizion's old friend in Gates to Infinity
*Gurdurr, leader of the Timburr Bros. and a minor boss in Gates to Infinity
*Scraggy, ran Scraggy's Savvy Moves and acted as a minor boss in Gates to Infinity
*Quagsire, former owner of Paradise land and ran Quagsire Assembly in Gates to Infinity
*Rampardos, ran the Box Buster in Gates to Infinity
*Cinccino, ran the Gift Shop in Gates to Infinity
*Swanna, ran the Post Town Inn in Gates to Infinity
*Victini, ran the V-Wheel in Gates to Infinity
*Munna, an antagonist from Gates to Infinity
*Gigalith and Chandelure, Munna's minions in Gates to Infinity
*Kyurem, an antagonist in Gates to Infinity
==Trivia==
*Certain dungeons may have a low amount of floors, but they are hard to get through matching the difficulty of high level dungeons from the previous Mystery Dungeon games.
*Instead of the player character, the partner disappears at the end of the story and is brought back by the player character. During the post-game, Mew temporarily takes the partner's place.
*This is the second Mystery Dungeon game that involves the final boss being a non-Pokémon enemy. The first was the Bittercold from Gates to Infinity.
*A feature in Super Mystery Dungeon is the music box which allows listening to the music in the game, depending on the console. Nintendo 2DS system allows listening to the music in sleep mode; Nintendo 3DS allows the same, but requires headphones to work.
*The second chapter's name changes depending on which Pokémon the partner is selected to be. Examples: if Froakie is chosen, the name will be Meeting Froakie and if Bulbasaur is chosen, the name with be Meeting Bulbasaur.
==Gallery==
Super Mystery Dungeon.png|Logo of Super Mystery Dungeon.
Category:Pokémon Mystery Dungeon
Category:Nintendo 3DS games
Category:Pokémon Super Mystery Dungeon