Pokemon Super Mystery Dungeon Here Comes The Hydroflames

Pokémon Super Mystery Dungeon: Here Comes The Hydroflames

Summary: Ian, once a human now turned Mudkip wakes up to find himself in a world only inhabited by Pokémon. Having no memories of his past, he meets up with a Fennekin named Patience who dreams of joining the Expedition Society. When an ancient evil awakens, turning any Pokémon in its way into stone. It is up to them to solve the mysteries of their past, and save the world from destrcution.

Note: Chapters posted here will not be chronological, it'll only be certain chapters that I think are worth reading for a first impression. Think of it as a preview, if you want to read the rest of the story, you can just search it up on fanfiction.net.


Chapter 1: The World Of Pokémon

...Ugh.

"Wake up."

W-what? Who are you? Where am I?!

"I know you would be confused as to what is going on but there is not much time to explain, by the time you hear this, I would be long gone from here. You may find it a bit... disorienting when you wake up. But all shall be explained in due time. Good luck, and see you on the other side!"

Before he could have asked anymore questions, a bright light engulfed his view blinding him. He closed his eyes as tight as he could and followed the voice's instructions:

To wake up.

When he opened his eyes again, he was greeted to a lush, green forest. He was laying on the grass.

W-what...? Where is this? I don't remember falling asleep in a forest...

Just then, he felt a sharp pain pierce his head he tried clenching his head with his hand, but lacked the energy to do so.

Damn, what the heck happened to me? He wondered. He tried as hard as he could to remember what had happened the previous night...

But nothing came up, his mind was a blur. He shrugged it off, he'll probably remember something in just a moment.

Thirsty... I'm so thirsty...

In the distance, he heard the sound of running water, it sounded like it was ahead of him. He tried standing up, but immediately fell face first onto the ground, looks like his legs are still numb. He started crawling towards the sound of water, using every ounce strength he could manage to pull himself.

After what seemed like forever, he saw what the source of the water was: A river. He quickly crawled towards it and dunk his head into the water and drank the water. He did find one thing odd however, he was sticking his head underwater longer than he should be able to, and he wasn't even holding his breath. But it didn't matter, this was the best water he has ever tasted.

When he was finally done, he lifted his head out of the water, feeling fresh and rejuvenated.

It was then, he noticed something in the water.

A blue creature, with orange fins on its cheeks stared at him through the water.

A Mudkip...? He could have sworn he didn't see any Mudkips in the water when he was drinking. Did it notice him while he was drinking him?

He tried reaching out towards the mudfish Pokémon, but strangely, the Mudkip reached out as well, as if mimicking its every move. When he touched the water, the water simply rippled, he did not touch the Mudkip, but it was still there. Getting more confused, he opened his mouth, and the Mudkip did as well, he stretched his arms, turned his head, all of it the Mudkip mimicked perfectly.

It was then he came to a very grim conclusion: That was a reflection, of himself.

No no no no no no no! He started to panic, he looked at the reflection once more, the Mudkip stared back at him again. It wasn't a wild Mudkip that was staring at him.

HE was the Mudkip.

His heart started pounding, he suddenly felt like he wanted to faint from the shock, but he couldn't. That would explain why he wasn't able to stand up, because he was a quadruped. He had too many questions racing through his head. He slowly breathed in, and exhaled.

"Alright, let's try to remember everything you can..." He said to himself. "My name... what's my name...?"

He thought of it for a moment and suddenly a name he assumed was his popped into his head.

"Ian, my name is Ian." He said. "What did you do last night?" Nothing appeared in his mind. "Where do you live?" Nothing. "What are the names of your parents?!" Once again, nothing.

Ian concentrated as hard as he could, hoping that something, anything would come into his head! But there was nothing.

He had lost all of his memories, and he was no longer a human.

Ian then realized if another possibility, he was dreaming. It makes sense! This is all just a dream and when I wake up, I'll be back to my normal, human self, possibly in a comfy bed. But now the question: How to get out from this nightmare?

He looked next to him, and saw a tree. A very stupid idea came in mind. He approached the tree and aligned his head right in front of it. Ian was going to knock his head as hard as he could, and hoped that it would cause him to wake up.

"Here goes nothing," He said to himself. He inhaled, and exhaled and counted to three.

One... two... three!

He slammed his head as hard as he could onto the tree bark, his head screamed in pain as he fell on his back onto the grass, clenching his head.

"Okay, maybe that wasn't such a good idea..." He said.

When he finally recovered, he realized that he was still right where he was, only now with a headache. The pain was real enough to tell him that he wasn't dreaming.

Guess this is it then... I'm going to be stuck as a Mudkip for the rest of my life then. He wanted to cry so hard right now, but forced himself not to, it wasn't going to change anything.

"Alright," Ian said. "I guess I just have to start walking through this forest, I'm been standing around here for a very long ti-"

"BEEP BEEP BEEP BEEP."

Ian quickly turned to the sound of the noise, and just then, as if they appeared out of thin air, three orange looking things floated in front of him, they head rectangular shaped heads and small arms.

"Beheeyems...?" He concluded.

The three Beheeyems faced each other and started flashing lights to each other with their hands. They then started to approach Ian.

"Uh... I assume this is friendly greeting?" He nervously asked.

The Beheeyems replied with one of them taking a swing at him, barely missing Ian's face.

"Can't we just talk about this guys?"

The Beheeyem swung at him again, this time hitting him, pain flowed quick through the rest of his body.

"Ah, to hell with this!" Ian said, as he dashed off in the opposite direction, hoping to lose his new foes in the forest. He clumsily tripped every five steps, still trying to get used to his new way of walking on four legs instead on two. Just then, out in the distance, he noticed a figure getting closer as he ran towards it. When he was close enough he was able to make out a few features.

Brown in colour, standing on two legs, has a leaf on his head and had a very long nose. Before he could make out any features, he underestimated his speed and crashed right into the Pokémon, causing the both of them to all straight on their backs.

"Good job Ian..." Ian smartly remarked to himself, as he got off the ground.

"What in the world is going on with you?!"

Ian's eyes widened in shock, did that Pokémon just talk...? B-but how is that possible?!

"What's the matter?" The Pokémon said, "You look like you've seen a ghost."

Ian was sure of it, that Pokémon, in fact, just talked to him in perfect English.

I think I'm going insane...

Just then, he heard the beeping from behind him again. The mudfish Pokémon turned around and saw the three Beheeyems chasing after him, one of them launched a white beam-like projectile from its hand and landed near their feet, taking them by surprise.

"Woah, what the heck?!" The Pokémon exclaimed.

The Beheeyem launched another attack, missing as well.

"We best get out of here!"

Ian nodded and followed after the leaf headed Pokémon. He has woken up in a strange world with talking Pokemons and with no memories of what happened to him.

As if his day wasn't bad enough, Ian was sure things are going to get even worse from here on out.

 

Chapter 10: Team Orion

Foggy Forest. What was once uncharted territory and barren, has now been turned into a popular tourist attraction for explorers. Years ago, Wigglytuff's Guild held an expedition to the area, hoping to discover the then alleged "Mysterious Fogbound Lake". The expedition was a success, with the guild finding Fogbound Lake, and it's most sacred treasure, a Time Gear and a mystical sight of a fountain formed by the lake's geysers. Since then, more and more explorers from different continents starting coming, eager to see the mystical treasure. Increasing demand had cause the Exploration Team Federation to place a rest stop at the entrance of Foggy Forest. Now, even with the Temporal Tower Crisis long behind everyone, the Time Gear taken to fix it, and it's Guardian, Uxie, vanishing without a trace. There was no sight of explorers coming to visit Fogbound Lake.

Absol walked silently through the dense fog, keeping her eyes and ears open. A gust of wind blew past her, causing her to shiver a bit. She never liked patrolling this forest, it's creepy environment and a potential ambu-

Absol noticed something in the corner of her eye, a figure, that quickly disappeared from sight. A threat? Most likely. She quickly scanned the forest, hoping to catch the perpetrator in action. When she heard a rustling noise behind her, she jumped back and launched a Dark Pulse at the source. Hitting a nearby tree, and something fell from the tree. Absol approach the object to examine it. A Substitute doll.

Absol sighed in annoyance, realising who it was.

"Very funny Greninja. I'm laughing so much right now." Absol said sarcastically.

"Well you seem rather jumpy. Attacking an innocent Substitute doll like that, that's not how Team Orion does things." A voice said.

Suddenly a figure appeared out of thin air, a blue figure, it's tongue tied around its neck like a scarf.

Team Orion, the Exploration Team Federation's go-to team whenever they needed something taken care of and for good reasons. With the team being Master Rank, they rivalled with even the alluding treasure hunters, Team Charm. While that team focused more on exploration and treasure hunting. Team Orion focused more on bringing outlaws to justice, with an impressive arrest record.

"What's the matter?" Greninja asked. "You look you've seen a ghost."

"I'm sorry..." Absol apologised.

"Is there something on your mind?" The ninja Pokémon asked.

"N-no! It's nothing...!" Absol hesitated.

"Absol..."

"Alright fine." She finally confessed. "I have a really bad feeling about this mission."

"You? A bad feeling?" Greninja said in surprise. "That's unlike of you."

She can agree with Greninja there, it wasn't like her to have such doubt in a mission before. To be honest, this whole mission feels suspicious. Why would the ETF, who are damn well aware of Team Orion's reputation, be sent to capture some Pokémon who's been harassing nearby explorers. It felt like the higher-ups weren't telling them the whole story.

"It just doesn't seem right." Absol explained.

"Don't waste your time thinking about it." Greninja said. "It's not for us to question our duties, we just keep our mouths shut, do whatever the pencil pushers back home tells us to, and get paid."

Absol couldn't really follow with her partner's logic, she wasn't in it for the fame and glory. Sure, the pay was good, the constant flow of Poké keeps the team running. But Absol only did it because it was the right thing to do. Protect the people, for it was the right thing to-

"Who goes there?!" Greninja exclaimed. Shifting into a battle stance.

Absol turned around to where Greninja was facing and in the distance, a lone figure. They both were unable to make out any distinctive features, but it was staring right at them, menacingly.

"Identify yourself!" Greninja yelled. The silence only being his only reply.

"Identify yourself!" Absol repeated. Expecting a reply this time, but still nothing.

The figure took out something and held it up high. A sudden flash of light blinded the two.

"Argh...! I can't see!" Absol exclaimed.

"It's only a Luminous Orb!" Greninja exclaimed. "Careful! We might be dealing with a potential thre-"

A sudden loud bang was heard, like lightning had just struck between the two. When the light finally faded. Absol eyes took awhile to readjust, when it finally did, she noticed that the figure had vanished.

"Damn! He got away!" She exclaimed. "We should split up and search for- what the?!"

When she turned to face Greninja, she froze. The ninja Pokémon had turned completely grey, one arm still covering his face. She couldn't believe her eyes.

Greninja had been turned into stone.

"Gre-Greninja!" She exclaimed. Moving closer to investigate. She started panicking, she was all alone, with whatever that just turned her partner into stone. She leaned her back against the now-stone Greninja, unable to think straight.

"Calm down, Absol... You can do this..." She said to herself. "Just breathe in... And everything will be alrigh-"

The last thing she remembered was seeing a dark, purple beam at the corner of her eye. And then everything went dark.

 

Chapter 26: Diplomatic Tensions

The PEACE (Protect Everyone in A Catastrophic Event) Accords took place on the XX day of the XX month of the XX year. It was established shortly after the Bittercold Incident that occurred in the Mist Continent. It was signed at the renowned Wigglytuff's Guild in Treasure Town of the Grass Continent by the representative organizations in each continent, excluding the Sand Continent, whom lacked an organization. The Helping Adventurous Pokémon Prosper Institution (HAPPI) of the Mist Continent was reformed into the Helping And Protecting Pokémon Institution.

The accords stated multiple things:

1. In the event of a crisis, all organization are to open their facilities for the public to take shelter.

2. All organization heads are ordered to contact the other heads and appoint an emergency summit at a desired location.

3. The organizations are to work together in order to overcome the crisis.

This, after multiple catastrophic events have taken place over the past few decades. This includes the Meteor Incident, the Time Crisis, and the Bittercold Incident.

As of today, the PEACE accords has not been initiated even once, and shows no signs of being initiated anytime soon with the world in a time of peace and prosperity.

"First of all, I would like to thank you two for coming here on such short notice." Ampharos said.

"To be fair, we've been here for about 4 days now." Keldeo said, annoyed.

Ampharos laughed nervously, feeling bad for leaving for such a long time.

"I apologize for that." He said. "For I had other matters to attend to.

"That's alright." Virizion assured. "We really enjoyed our time looking around Lively Town."

"That's because you're not the one getting supplies for the journey home..." Keldeo mumbled.

"Either way, we have urgent matters to discuss. Please, follow me."

Ampharos lead the two Musketeer Pokémon up a flight of stairs and into a room with a table, behind it on the wall was the Expedition Society emblem: A circle within a circle with wings. Verizion thought it wasn't the most creative, but then again, HAPPI didn't even have an official emblem.

Ampharos closed the door and ushered the two Pokémon to sit down. The lighthouse Pokémon took out a piece of paper and placed it on the desk.

"I'm sure you know what this is." He said.

Virizion inspected it and noticed that it was a drawing, a drawing she was far too familiar with, the two Pokémon that made the turning into stone incidents a major problem.

"Team Orion." She replied.

"It was one heck of a surprise." Keldeo said. "The Grass Continent's finest, turned into stone like it was nothing."

"Any leads on the culprit?" Virizion asked.

"A few Pokémon had been detained, but all of them weren't who we're looking for."

"Damn..."

Ampharos could hear the pain in Virizion voice. He had read the reports, the Ragged Mountains Massacre. An entire dungeon, all of its inhabitants, turned to stone overnight. It was the reason he had called HAPPI, he had reason to believe the culprit is somewhere on the Water Continent. All he had to do was request for some help in catching the criminal, catch the criminal, bring him to justice and be done before summer was over.

"Mutual gain", as he liked to call it.

"You said you were investigating this as well?" Keldeo asked.

"Yes, I believe the culprit is someone in this continent."

"WHAT?!" Keldeo and Virizion exclaimed.

"One of my... associates, believes that the culprit behind these turning to stone incidents is residing here."

"Do we know where?"

"No, I investigated the area where my associate suspected, but it proved fruitless."

"That's unfortunate." Verizion said.

Just then, Ampharos Expedition Gadget rang, much to his surprise. He took it out and answered it.

"Yes? Yes, this is Ampharos speaking. What? When?! Alright, I'll be there as soon as possible." Ampharos hung up the gadget. Slamming his hand on the table.

"What's going on?" Keldeo asked.

"It was the Rescue Team Federation of the Air Continent." He said. "The inhabitants of Pokémon Square have been turned into stone."

Patience jolted out from her bed, sweat dripping of her face, her heart beating really fast, her whole body shaking.

Again, she was having that dream again.

Patience's head was spinning, she couldn't think straight. She went over to the other side of the room and took a sip of water from a basin.

Much better.

She took a deep breath, and exhaled. It was third time she was suffering from some kind of nightmare. She honestly didn't really know, she could never remember the details of the as soon as she woke up, but it always left her agitated.

Great, just great.

She looked out her window and saw the moon, illuminating the night sky above, it was a really pretty sight.

She looked down at her twig necklace at held it close to her. It seemed to be a habit now, she would always hold on to the necklace whenever she felt insecure or nervous.

Maybe it's because it reminds me of Ian. Like a part of him is always by my side, always there to comfort me.

She shook those thoughts out of her head, and decided to go back to sleep.

Tomorrow's going to be another great day.

 

Chapter 50: Night Watch

Ian and Patience watched as Buizel hung up the new Expedition Society group photo in the Crew Room after dinner. They had taken the picture earlier this afternoon, a Pokémon by the name of Meowth had came by with a camera. What Meowth didn't realize however was that the camera was not in proper working condition and every time the Expedition Society prepared for the photo to be taken, the camera would break down and had to be set up again. Adding to that everyone was standing under the hot summer sun, it wasn't an enjoyable time for anyone.

"There, all done." Buizel said.

Ian and Patience took a step closer to examined the picture, it looked better than he expected. Ampharos, Mawile, Archen and Gadget stood professionally side by side, only giving a small grin for the camera. Buizel had the most outlandish pose, head facing down and arm and elbow raised in a single direction, as if he was sneezing. Bunnelby was supposed to look natural in the photo, holding an apple and casually eating it. But Swirlix saw the apple and wanted to swipe it out of his hand with his mouth, but she mistakenly also bit Bunnelby's hand, which led to the appropriate reaction of him screaming in pain. Jirachi simply floated there, half asleep and oblivious to the whole thing. Glaceon stood in front of the group, wrapping her arms around both Ian and Patience and happily smiling, the two looked at her and merely gave an awkward smile.

"I have to say, this has got to be the best group photo thus far." Buizel commented.

"How so?" Ian asked.

"Well, there're more... unique expressions."

Ian looked over to the previous group photos hung on the wall and noticed that Buizel was right. They were all mostly the same, the Expedition Society members smiling and looking straight at the camera. The previous most recent photo was when they started becoming more enthusiastic and relaxed.

"Welp, I think you two should get going, your night watch starts in five minutes."

"Wait, night watch? What the heck is that?" Patience asked.

"Oh, nobody told you? Every night, two of us take turns patrolling the streets of Lively Town to ensure the safety of the residents. And according to the imaginary list, you two are up next."

Ian expressed a look of surprised when Buizel mentioned they had to patrol Lively Town at night, Patience as well.

"How long do we have to patrol?" Ian asked.

"About four hours." Buizel answered.

So much for getting a good night's sleep after this...

Ian sighed and waved for Patience to get moving. Buizel wished them good night before making his way to his room. The two partners made their way to the entrance of the Expedition Society Headquarters, opened the door to the outside world and left. There were still a few Pokémon roaming the streets of Lively Town at night, mostly Pokémon on their way home or closing up their shops, the town was quiet, with only the voices of a few Pokémon talking about their days before going their separate ways. Ian and Patience split up and started making making their rounds around town, walking back and forth, keeping an eye out for anything suspicious. Occasionally, a resident would ask them what were kids wandering around this late at night, in which Ian and Patience had to explain that they were Expedition Society members. The first hour passed, then the second, then the third...

Ian yawned as he passed by the town's entrance for what seemed like the fiftieth time now, his eyes were starting to ache and he couldn't concentrate. He wished that he had gotten some Chesto Berries from his bag to keep himself awake.

Couldn't they just have gotten someone else for this? Ian grumbled in his head as he made his way back to the town plaza once more. At this hour, Lively Town is shrouded in complete darkness, the only thing illuminating the town was the moonlight and stars that covered the calm night skies, Patience would've love to sit down and just gaze at the stars.

Speaking of Patience, where is she?

The mudfish Pokémon has not seen her for quite sometime now, the last time he saw Patience was just over a hour ago when they both bumped into each other while walking through the streets. Nothing from her since then. Ian went through the town once more, searching every side alleys that Patience might be in, after multiple rounds it proved fruitless. For all he knew, Patience was probably exhausted and had already went back to their room and fallen asleep, leaving the mudfish Pokémon wandering around in circles for nothing. Although, there was still one place he hasn't checked yet.

The docks.

Ian broke into a stride and made his way to the docks. When the mudfish Pokémon reached the stairs that led to the lighthouse, he saw a small, figure sitting by the edge of the pier. It didn't take long for Ian to realized it was Patience. She was looking up in the sky and gazing at the stars.

Guess my hunch was right.

"So this is where you've been." Ian said. Patience turned her head surprise when she heard the mudfish Pokémon's voice.

"Oh, I didn't hear you coming." Patience said.

"And I didn't know you could take a break to watch the stars." The mudfish Pokémon lectured.

"Oh stop being such a party pooper Ian," Patience said. "it's not like anyone's going to know. Come on, kick your feet up and just relax."

She does have a point.

Ian simply sighed and decided to follow the fire fox Pokémon's advice. He walked up to her side and sat down next to her. The two Pokémon began gazing at the night sky together, they remained quiet for what felt like a long time before Patience decided to speak up.

"This sight really reminds me of Serene Village." She said.

"How so?" Ian asked.

"The starry sky, sitting under that big tree..."

"Ah, now I remember." Ian recalled also being with Patience under a starry sky a few times. Twice to be exact. The first was when they made up and reconciled after having an argument, the second was when they became an expedition team.

That felt like ages ago...

Patience inched herself closer to her partner and laid her head on his shoulder. Ian was surprised for a moment but immediately relaxed, honestly at this point he shouldn't really be surprised with Patience.

"I miss Serene Village..." Patience said as she started to frown. "I miss my pops, I miss our classmates, I miss everyone..."

Ian couldn't agree more, every day he still thinks about the villagers back in Serene Village, the Pokémon that had gave him a place to stay and cared for him.

Especially Nuzleaf.

The mudfish Pokémon placed his hand on Patience's head and began stroking it. The warmth of her fur felt nice.

"Me too Patience, me too." He said.

The two partners remained in their positions for quite awhile, until Ian let out another yawn, realizing that he was getting even more exhausted. They should probably head back home now.

"Hey Patience..." Ian turned his head and noticed the fire fox Pokémon had fallen asleep, snoring away on his shoulder. He gave Patience a slight nudge to wake her up, but she remained sleeping. The fire fox Pokémon didn't look like she was waking up anytime soon. Ian sighed, knowing what he had to do. The mudfish Pokémon gently lifted Patience and slung her over his body, Ian felt a sense of deja vu, although there was a slight difference.

Good lord, has Patience gotten heavier? Ian thought to himself. He still remembered Patience being much lighter when he had carried her back in Serene Village. It's probably Swirlix's cooking.

Ian made his way back to the Expedition Society Headquarters, went back to his room, placing Patience into her bed before collapsing into his own bed, immediately falling asleep as he ends a tiring night.