Pokemon Mystery Dungeon: Rise of Darkness

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Pokemon Mystery Dungeon: Rise of Darkness is the sequel to Pokemon Super Mystery Dungeon. It contains all the Pokemon from Generation 1 to Generation 7. The game also features Mega evolutions, Giga Moves, Primal Reversion and Forme Changes. The game is mostly based on the Mystery Dungeon exploring. This game also features a never-before seen mechanic that the Mystery Dungeons will change it's layout in a specific time spot.
Plot
Prologue: The Dream Begins
Like the start of every Mystery Dungeon game, the player is being taken to the world of Pokemon. However, the voice the player is hearing talks about it has been searching for the player for millions of years. The voice then takes the player to the world of Pokemon, where it wakes up and realizes that he's been turned into a Pokemon. Shocked by this, a small Pokemon, the partner, hears the player and decided to come towards the player. He then asks the player where he is from, but he wouldn't believe that the player was a human. The partner then walks off, but the player decides to follow him into a Mystery Dungeon. Being annoyed by the player, the partner decides to walk away from the player, leaving him lost inside of the Mystery Dungeon. After completing the Mystery Dungeon, the player then finds the partner in Moki Town, the Home Town of the partner. Still not really trusting the player, the partner decides to show the player around Moki Town. Suddenly, a Roserade comes towards the player, and says it needs their help, because her baby has fallen inside of a hole. Agreeing the quest, the two set out into the Mystery Dungeon and save the Budew. Liking the way on how the player acted in the Mystery Dungeon, the partner asks if he would like to join the Expedition School, where they explore Mystery Dungeons. The two then join the Expedition School, where they meet Croagunk, Alolan Vulpix, Goomy, Aron, Sandshrew and Meowstic, the tutor. 
Chapter 1: The Power of Two
Being new to the Expedition School, the player and the partner were very nervous. Croagunk and Sandshrew were the bullies of the school, but they were secretly cowards. Croagunk and Sandshrew then asked the player and partner if they were brave enough, and they would prove it by going into Mystery Cave, a big Mystery Dungeon. Agreeing to this, the player and the partner go to Mystery Cave, but then they are attacked by a Graveler during the dungeon. When they beat Graveler, he offers to get them out of the Dungeon. Croagunk and Sandshrew were very surprised to see the two get out with no harm. Then, back in the Expedition School, they go in a few Mystery Dungeons. After having cleared the Dungeons, the school day was over and the player and partner went back in town. The player would then ask the partner where he lived, and the partner said he forgot. He then explains that he was born in the forest, and had intentions of coming to town. He then decided to steal in order to survive. The player and the partner then go to the forest where the partner was born, and slept there.
Chapter 2: The Chase
When the player woke up, he noticed that the partner was gone. The player then decided to get inside of the Mystery Dungeon part of the forest, where, after he completed the Dungeon, he found the partner being fainted. The partner then explains that Croagunk and Sandshrew stole his berries and attacked the partner after he went and checked. The player then explores the forest before going inside the Mystery Dungeon part of the forest again. He then found a small stone, which could talk. The stone then talked about a darkness coming to this world. Not understanding what the stone was talking about, the player put the stone inside of the Bag. He then went inside the Mystery Dungeon part of the forest again. Once he found Croagunk and Sandshrew, the two challenge the player to a battle alone. After being beaten by the player, the two bullies admit that they only stealed the partner's berries because someone told them too and they thought it would be a nice test. The player then takes the berries back to the partner, where the partner is pleased to see his berries back. The stone then shines, and a bird flies on top of the forest. It was Ho-Oh, the Legendary Pokemon. The player and partner then return to Moki Town, where they tell everyone about their adventure, but not about Sandshrew and Croagunk stealing their berries. 
Chapter 3: Two Legends: The Stone and the Legendary
After telling everyone the story, the player and the partner decide to go back to the Expedition School. They then help Meowstic organize, but then, a book drops on top of the player's head. The player reads the book about an old myth, about a war which happened a long time ago, where humans and Pokemon thought. It was a time when humans were still a part of this world. It was actually a reference to the Kalos War from Pokemon XY. During King AZ's secret weapon explosion, a realm to another world was made. In the realm to another world, the humans had all died from the explosion, but a few Pokemon survived somehow. 200 years after the war, Jirachi was created, and protected this land. However, Darkrai was created too, and made havoc all over the land. Jirachi tried to stop Darkrai from causing more havoc, but Jirachi was hit by one of Darkrai's beams, and turned into a stone. The player then remembers the stone it saw in the forest. The player then shows the stone to the partner and Meowstic, where Meowstic was very interested about the stone. The stone then talked to the player, where it explained that the legend was true and the stone was Jirachi. Jirachi then floated towards a volcano, where the player, the partner and Meowstic all entered inside a Mystery Dungeon. After all having completed the Dungeon, the gang was then attacked by a Houndoom, who wanted to take the stone for itself. After defeating the Houndoom, the Houndoom explains about the stone, that it wants to take it because someone commanded it to do so. The Houndoom then leaves, and the hero, the partner and Meowstic all find the stone in the center of the volcano, where a portal appeared. The hero, the partner and Meowstic all enter the portal, where they find Shadow Lugia. After defeating Shadow Lugia, the gang finds a strange star. It was revealed that the star was a Shadow Star, which made other Pokemon turn into darkness. Jirachi, as a stone, then healed the star to make it a Light Star. The gang then returned to Moki Town. 
Chapter 4: The Ancient Egypt Adventure
Jirachi tells the player and the partner about the Shadow Stars, how they were scattered, during Darkrai's rampage. The three then decide what they have to do: Leave town. They then leave the town after saying goodbye to everyone in the Expedition School. 5 hours later, the three find themselves in a desert. They then go and sleep by an oasis, where the player has a nightmare about Darkrai. He then wakes up, and remembers something. He then tells the partner that he heard a voice when he was being transported to this world. The partner then finally believes him about being a human, and they make themselves into a Pyramid, which is also 2 Mystery Dungeons in one. After completing the first Dungeon, the three are attacked by the same Houndoom from before, but Mega evolved, after defeating him, Mega Houndoom returns to normal and runs away. After completing the second Dungeon, they are attacked by Raikou. After coming to his senses, Raikou joins the team for this time, and then the gang are being attacked by Dark Reshiram, who, after being defeated, says that he was corrupted by Darkrai. Reshiram then shows them the way to the Shadow Star, and then Jirachi heals the Shadow Star. Jirachi then says that there are 2 more Shadow Stars to go. They then take off, to the Mystery Dungeon part of the desert after saying goodbye to Reshiram and Raikou. 
Chapter 5: The Airborne Showdown
When the hero, the partner and Jirachi find their way, they meet a Ampharos who runs a transport service to Skyhigh Town, which is a Town who contains multiple Flying-type Pokemon. The gang then fly to Skyhigh Town, where a black mist cloud appears. The black mist cloud turns into Darkrai. Jirachi then challenges Darkrai to a battle, but Darkrai refuses to battle a "stone". Darkrai then recognizes the player, and wants to battle it. The partner asks if he can battle too, but Darkrai calls him a "weakling Pokemon" and battles the player instead. The player loses, but Jirachi regains the player's strength, and the player then wins. Darkrai calls this a cheat. He then goes back into the dark mist cloud and leaves. Then, all of Skyhigh Town thanks the player for getting rid of Darkrai. Then, the player, the partner and Jirachi all go towards a flying castle which are 3 Mystery Dungeons in one. After completing the 3rd dungeon, a huge battlefield appears, and Mega Rayquaza was summoned. After beating Mega Rayquaza, Mega Rayquaza offers the heroes the Shadow Star, then, Jirachi heals the Shadow Star and it becomes a Light Star. Then, Mega Rayquaza lets the player, the partner and Jirachi fly off to Iternal Space, which contains the last Shadow Star.
Chapter 6: Iternal Space's Iternal Evolution
After arriving in Iternal Space, the heroes retrieve the Mega Stone (Depends on what Pokemon you picked, and will not be given if you don't have Pokemon which can Mega Evolve), and then enter the Mystery Dungeon in space. It was 6 Dungeons in one, after you completed the first one, you would battle Suicune. After the second one, you would battle Latias and Latios. After the third one, you would battle Dialga and Palkia. After the fourth one, you would battle Zekrom. After the 5th one, Yveltal (With assistance of Xerneas, who wants to stop Yveltal) and after the 6th one, Solgaleo and Lunala. After having beaten all the dungeons, the player, the partner and Jirachi see Mega Mewtwo X, and would challenge them to a battle. The player and the partner would lose, but Xerneas from before would power up the two and they would evolve into their final evolutions. The two then beat Mega Mewtwo X, and Mega Mewtwo X hopes they beat Darkrai soon. A portal would then be seen, which the player, the partner and Jirachi would gain access to. They then arrived into the Darkness Realm, which was a vision of the future how it would be if Darkrai invaded.
Chapter 7: The Final Showdown... Darkrai!
After arriving in the Darkness Realm (Which happens to be a Mystery Dungeon), the partner is sad to see the future like this. He then motivates the player into going and defeating Darkrai as soon as possible. They then arrive inside of the Dungeon, where they would fight Dark Moltres, Zapdos and Articuno, Shadow Mewtwo, Shadow Ho-Oh, Dark Dialga and Dark Palkia. After having beat all of them, they complete the Mystery Dungeon and they find out that Darkrai has corrupted Arceus and putting itself inside of it's body. Darkrai (Now called Dark Arceus) challenges both the player and the partner for a battle. After having putting Dark Arceus' HP low, it defeats the hero and the partner by using Draco Meteor. The player keeps thinking about what would happen to the Pokemon World if he was defeaten, and makes a wish for all of us to regain our strength. Because of this wish, Jirachi gets out of the stone and turns into it's normal body, Jirachi, being touched by the player's wish, regains the player and the partner's strength. If you recieved a Mega Stone before entering Iternal Space, you would Mega Evolve. If you didn't, then you would shine brightly. After having beaten Dark Arceus, he faints and Darkrai gets out of Arceus' body. After beating Darkrai, Darkrai slowly stumbles to tell the gang that the only reason it wanted to destroy this world in the first place, was just so that he could create a new world for only himself. The Darkness Realm then suddenly shines, and it explodes. The hero, the partner and Jirachi then wake up back in the partner's home forest, but the hero and the partner are back to their original forms. Suddenly, the player turns into stone, because of the Draco Meteor from before. Dark Arceus actually powered up the Draco Meteors which would hit the player so that he would turn to stone. The player then says sorry to everything he has caused the two, and turns completely into stone. Saddened about this, the partner leaves and goes back to the place where the player and the partner first met. The partner then wishes for everything to turn to normal. Jirachi then tries to cheer him up, but it fails. He explains that all his life, he/she's been wanting to go on an adventure for so long. And he finally achieved his dream, and the only thing he wanted was his only friend... the player. Jirachi, being touched by the care of friendship, gets the power to revive the player, and the player decides to stay in the Pokemon world forever.
Starter Pokemon
Pikachu
Bulbasaur
Charmander
Squirtle
Vulpix
Larvitar
Chikorita
Cyndaquil
Totodile
Sentret
Pancham
Froakie
Chespin
Fennekin
Tyrunt
Riolu
Litten
Rowlet
Popplio
Rockruff
 Mystery Dungeons
Name
When visited
Boss
Odd Cave
Prologue (TWICE)
N/A
Mystery Cave
Chapter 1
Graveler
Gale Forest
Chapter 2
N/A
Gale Forest Outskirts
Chapter 2
Croagunk & Sandshrew
Mt. Lunacux
Chapter 3
Houndoom, Shadow Lugia
Reef Pyramid
Chapter 4
Mega Houndoom
Old Catacombs
Chapter 4
Raikou, Dark Reshiram
Cubegrain Desert
Chapter 4
N/A
Mist Castle
Chapter 5
N/A
Mist Basement
Chapter 5
N/A
Mist Castle Top
Chapter 5
Mega Rayquaza
Iternal Space: A
Chapter 6
Suicune
Iternal Space: B
Chapter 6
Latias and Latios
Iternal Space: C
Chapter 6
Dialga and Palkia
Iternal Space: D
Chapter 6
Zekrom
Iternal Space: E
Chapter 6
Yveltal
Iternal Space: F
Chapter 6
Solgaleo and Lunala
Iternal Battlefield
Chapter 6
Mega Mewtwo X
Darkness Realm
Chapter 7
Dark Arceus/Darkrai
There are also different Mystery Dungeons, but you do not get to access them. They are only seen as a part of the story in Chapter 1.
Trivia
Dialga makes a reference to Pokemon Mystery Dungeon: Explorers of Sky/Time/Darkness before his battle, his quote is "I have heard of you... You.. You give me memories of a time when I caused havoc... There was also this human who turned into a Pokemon, just like you... And he stopped me from doing more havoc..."
In the Darkness Realm, there is a area which has not been seen inside of the Pokemon world, it's location is called "Tower of Misery", where you fight Yveltal.
You can re-challenge bosses in the Boss Rush game mode, and even a secret boss, Arceus himself.
Unlike the other Mystery Dungeon games, this game has no post-game.
Croagunk and Sandshrew are references to Koffing and Zubat from Pokemon Mystery Dungeon: Explorers of Sky/Time/Darkness.
After you beat the game, you will be able to go back in Mystery Dungeons, and there will be Legendaries who will be wanting to join your team.
Shadow Lugia is a reference to Pokemon XD: Gale of Darkness.
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