Clockwork Saviors Story

This page details the full story of Fakemon Mystery Dungeon: The Clockwork Saviors. Be warned that this page spoils the entire game (though that doesn't matter much because this is all just a fan made idea). 
Chapter 1: The Adventure of a Lifetime
The game begins with a personality test. You can see it here so you can take it for yourself. The player wakes up as a Pokemon. You meet your partner who notices that you are wearing a harness with a strange green gemstone on it. After a failed attempt to remove the harness, the player and their new partner travels to Timber Town. The two work together to join the Rescue Elite by completing the Training Pit. In terms of gameplay, this is your tutorial of how to play. You join up with Team Leaf and meet the other teams: the mean Team Branch led by Gauntlight, the kind Team Root led by Blitzodi, and the veteren Team Seed led by Medisheep. Each of the other team leaders explain something important: Gauntlight teaches you about the Mission Board, Blitzodi teaches you about the Shop, and Medisheep teaches you about Special Missions. The game tells you something that Gauntlight didn't say: the colors of the missions show what they are. Blue Missions are Regular, Yellow Missions are Story, and Pink Missions are Special.
Chapter 2: Danger in the The Desert
 Your first Story mission involves going to a Time Temple where a Robbit has gone missing. They enter a Time Temple, which reacts to the player's gemstone and glows so bright that Team Leaf passes out. When you exit the temple, both of you find it odd that you are in a desert. Shockingly, you realize that you have time traveled to the Egyptian Era. You try to reactivate the temple, but it seems that you are stuck in the past until your Story mission is done. This affects what missions you get. The Story Mission for the Egyptian Era takes place in The Pyramid. After defending Anubliss from an Evilvolved Pokemon, you earn your first Guardian Power. He tells you there is someone else with a stone like yours. You are not alone. You have a mysterious dream, with the shadow of a mysterious turtle in the distance. Your partner doesn't know about that Pokemon and insists they tell Bishroud what happened the previous day. 
Chapter 3: Party in the Past
On the way to meeting with Bishroud, a distress call comes from the Time Temple. Your partner thinks how odd it is to have to save someone else. You must go to save the Pokemon by travelling to the Eighties Era. After defeating another Evilvolved, the Timeline Guardian Dancilly says that your gem is called the Good Time Gem. He also says that the second stone that Anubliss mentioned is called the Bad Time Gem. When two unite, give up the fight. When you return home, you finally talk to Bishroud. He explains that the Good and Bad Gems were created by a Legendary Pokemon named Shellstream. Shellstream created them to contain the good and bad futures. The two gems together could have the power to control or destroy any timeline. You manage to leave him dumbfounded when you tell him about your dream. He thinks that your gem is the Good Time Gem and that the shadow was of Shellstream. When you leave, you find out that Team Branch has gone missing when they went to the Time Temple. Your partner says that while Gauntlight and his crew is annoying, even they don't deserve to be kidnapped.
Chapter 4: A Gauntlight in the Castle
You travel to the Gothic Era so you can save Team Brranch and the third Timeline Guardian. The Timeline Guardian named Dragonkeep gives you another Guardian Power and also warns you that darkness is on the rise. Team Branch comes back to the present with you, where Gauntlight grudgeingly thanks you for saving him.
Chapter 5: Ghost in a Ghost Town
On the way to the next era, a strange ghost appears near you. You have no idea what it is and you must have it as a partner through the Cowboy Era. After meeting with Warmadillo, you find out that this ghost is a Smitaphent. It disappears following the revealation that this Smitaphent is tied to the identity of the villain. You go to bed and have a nightmare. You wander through an abandoned house alone hearing crying. At the end, you find a Smitaphent sobbing in a corner. The screen fades to white as you hear: "Why did it have to be him?"
Chapter 6: The Melting Ice Age
The danger continues as you make your way to the Ice Age Era. Blitzodi and her team comes with you because she wants to experience time travel (though she tells Bishroud that she is going as backup). Blitzodi and you work together to defeat another Evilvolved Pokemon and earn Mammolith's Guardian Power. He doesn't give a clue to the story because Mammolith can't speak. You have another weird dream where you are teaming up with a Boofalo to save a Pokemon from some mean Steel types. This battle is a forced loss by the way. You fail to save him as the sky turns blood red. You then reset the time loop and repeat the battle. This time, you succeed after Boofalo evolves into Bishroud. You find out that this Bishroud is the one who you know and that a strange purple hole has opened up in the sky. After awakening, Bishroud says he had the same dream as you and that he wants to join your team. Bishroud will now fight alongside you.
Chapter 7: Let's Do the Time Rip Again
You travel into the next era to meet with the sixth Timeline Guardian, Ninjill. But when you arrive, you see that a purple hole has opened up in the sky. It looks just like the one from your dream last night! Bishroud says that it is a Time Rip which is the special power of the Bad Time Gem. Time Rips are able to corrupt the past and cause problems for the future. Fighting your way through the Japanese Era, you meet Ninjill after stopping another Evilvolved. Ninjill tells you how your gem can help Ninjill close the Time Rip. When you go to do it, a red glow appears inside it. As you leave, Ninjill warns you that the truth shall be revealed soon. That night, you have another nightmare. You're back in the house from Chapter 4's nightmare except this time it's burning. Also, you have to fight against strange Shadow Pokemon. At the end, you see another Smitaphent who is crying out for help. A voice calls out from behind the wall saying that he is here to save the day. Loud banging is heard and the building starts to collapse. You wake up just as the building is about to crush you, hearing the Smitaphent scream in pain.
Chapter 8: Greeting Ghosts in Greece
Before you head to the Time Temple, you tell your partner about your nightmare. He clearly is acting skittish, almost like he is hidding something. The trip through time goes wrong as a black shadowy creature appears and grabs you. Your partner and Bishroud try to fight it, but get knocked out. You arrive in the Greek Era where you must fight without your partners. A Gardome and Huskeen joins you for this era. When you make it to the captured Pokemon, a Shadow Eyed Manpsy appears out of nowhere. Crazier still, he's wearing a harness with the Bad Time Gem inside! After another Evilvolved is defeated, Manpsy flees through a Purple Time Portal saying that he has a score to settle. Collostone tells you to go home. The time has come to learn what is going on. When you return to the present and tell your friends about the Manpsy, Bishroud finally explains what is going on. In the past, Bishroud and Manpsy were the first Rescue Elite team called Team Sprout. They went to stop a fire at a house. Manpsy tried to cut his way to a Smitaphent, but his arrogence and haste led to the Smitaphent's death. After that, Team Sprout fell apart and Bishroud retired to become Rescue Elite's commanding officer.
Chapter 9: Friends Far into the Future
There is only one more Timeline Guardian to meet with: Cybersect. Bishroud is hesitant because he doesn't want to fight his former friend. You arrive in the Future Era. The evil Manpsy is encountered at the end who explains the rest of his backstory. After he left Team Sprout, he found the Bad Time Gem. He began hearing the voice of a creature calling itself the Dark Keeper, the Destroyer of Time. Each Time Gem contains a powerful entity: The Good houses Shellstream while the Bad houses Dark Keeper. Dark Keeper said that if Manpsy helped him destroy the timeline, they would become the most powerful creature in all of time. He of course agreed to that and off they went to weaken the timeline to prepare for its destruction. You then note that it's odd how he seems to not have a Pokemon with him to Evilvolve. He responds:"Why would I do that when you have brought one for me?" And then, your PARTNER Evilvolves! You manage to beat him and save Cybersect. Manpsy retreats through another Time Portal, saying that it's already over...
Chapter 10: Writing The Pages of History
As you return to the present, you see that the present is not what it was. The sky is pitch black, the Teams are in bad shape, and Timber Town is in ruins. As you learn, Manpsy has transformed the eras into a massive black hole that will absorb and obliterate everything. Using your Good Time Gem and the Time Temple, you transport everyone to Manpsy's base: the Dark Hold. However, transporting to a place with so much darkness and with so many people with you takes its toll. The Good Time Gem cracks, making it dorment and useless. At the Dark Hold, Manpsy laughs as he says that he has been powered up by the Dark Keeper. Surronded by darkness, he battles you himself with the full force of evil. The battle is interupted, however, when the Dark Keeper breaks free from the Bad Time Gem. Manpsy lies asleep on the ground as the Dark Keeper proceeds to mop the floor with you. Just when he is about to destroy you, Shellstream breaks out of the Good Time Gem and summons a white shield to protect you. He grants you the ultimate power: the White Wings that gives you higher stats than normally possible. With this new power and the party fully healed, the Dark Keeper gets defeated in an epic final battle. 
Ending
The Dark Keeper says that he will never be defeated because their will be darkness as long as there is life. Shellstream's response is: "True. But you shall not be part of that darkness." The Dark Keeper gets vaporized by you performing the White Wing Whirlwind. Manpsy wakes up and he's no longer evil! Shellstream teleports everyone back to Timber Town. A big party is thrown to celebrate your victory. He states that evil has been defeated and you have destroyed the Dark Keeper once and for all, leaving him as just a memory. Fusing pieces of the Good and Bad Time Gems to form the Singularity Time Gem, he attaches the Time Gem to the Time Temple. Shellstream tells you that the Singularity Time Gem unlocks the ultimate power of the Time Temple: the ability to change a Pokemon's past. The Dark Keeper's presence opened a lot of Time Rips throughout history and the Rescue Elite need to patch them all up. Anyone that they fix the Backstory of is able to join the team. As he leaves, you and the Rescue Elite look out into the sunrise. Your partner says how he's always wanted to be part of something bigger, and that wish has now come true.
The End...Of the Main Story
Post Game Story
You explore around to fix the timeline as best as you can. The final main Backstory is learning that the evil Pokemon Darkrai started the fire that changed time forever. Darkrai is a "true final boss" and he is extremely tough. Once you collect Manpsy, Shellstream thanks you and says that all the damage that Dark Keeper has ever done has been reversed. He thens says that he will join you so that you have the ability to relive your amazing adventure as many times as you want. 
The End