//------------------------------//
// What comes in the Night 
// Story: Pokémon/Digimon Mystery Dungeon: The Adventure Begins 
// by StormPhoenix246 
//------------------------------//

It’s only been a couple of days since Tom met Team Elemental and stopped a crime spree of thefts. After everything was returned to its rightful owners, things began going back to normal, except for the two extra additions to the town.

Sandile has spent his time over at Sugarcube Corner with Pinkie Pie, usually helping her in the kitchen. It did not seem like he was unhappy with his new living arrangements the last time Tom saw him. The desert crocodile has been seen assisting Pinkie with her orders or relaxing on the side with Gummy. All and all, it looked like things were looking up for the former thief. And the other thief’s time in Ponyville hasn’t been too bad either.

Since she came to live with Tom and Twilight, Emolga has been starting to grow close to them. At first, she kept to herself, barely uttering a word to any of them, and only ever spoke when she came out to eat. Besides that, she would always be up in the tree alone with her thoughts. Tom knew that she needed some time to herself in this new environment, so he left her alone. After a while, each of the mares interacted with her differently, but she was beginning to become comfortable around them. Comfortable enough that she began to eat with all of them at the library, meet other Pokémon at Fluttershy’s cottage, and help with Tom’s training. She was beginning to become a member of this family that were strangers to her before.

Pancham and Shelmet were still MIA, but Tom just figured the two were probably enjoying their freedom from Slaking. With everything quiet around Ponyville, he decided he’ll worry about them if they cause trouble. And since he hasn’t heard back from Team Elemental in a time, he decided to continue his training.

Right now, he’s back in the Everfree Forest training with Emolga as his opponent, while Shinji and Pikachu are off on the side watching. Tom was hurling razor-sharp leaves into the air while Emolga was dodging the projectiles. He was a plant Pokémon with a bell-shaped body. He had a gaping mouth with pink lips and two sharp teeth. His semicircular eyes appear directly under his mouth and he had several dark green spots on his body. On either side of his body was a large green leaf. Covering his mouth was a leaf with a long, brown, yellow-tipped vine growing out of it.





Normally, he wouldn’t be fighting an Electric and Flying type with Grass and Poison type, but Shinji suggested that he needed to fight while at a disadvantage. It was a way to combat adversity despite the overwhelming odds. This wasn’t an uncommon concept for Tom, since that’s the base for almost every anime he’s seen, so he just followed his master’s orders.

“Don’t lose focus, Tom. Your opponent won’t let up just because you’re at a disadvantage. In the Pokémon world, you have to adapt to the moment or give up your life.” Shinji said while eating an apple from his lap.

Tom hurled another leaf at the flying squirrel while saying, “I know.” He was getting tired of this hit-and-miss situation he was in. His energy was also starting to run low.

“Missed again.” Emolga taunted, avoiding another Razor Leaf from the Flycatcher Pokémon. This was starting to enrage the shapeshifter as he hasn’t hit the squirrel once.

Emolga saw his enraged face and just laughed at the expression he made. She found the whole thing kinda funny but didn’t allow that to distract her in this battle. This may be just a sparing match, she wasn’t going to lose.

She soared through the battlefield, leaving faint afterimages behind her. Tom saw her gliding towards him, ready to deliver the super effective move, so he switched from offense to defense. He raised his leaves as a glass barrier appeared around him to protect against the incoming attack. 

Emolga collided with the defense barrier at top speed and slammed into it multiple times. Tom took damage from the onslaught of flying attacks, but the damage was reduced thanks to the barrier. While taking more and more hits, he was thinking of a way he could turn this battle around and thought of something. It wasn’t a perfect plan, but it was the only thing he could think of.

Once Emolga was done attacking, she soared away from the plant and waited for his next attack. She and the others were surprised to him simply raise both his leaf arms. He was asking her to come at him with everything he got. This took everyone by surprise, but Emolga wasn’t going to squander this chance. 

She glided down and delivered another Acrobatics attack, hitting the shapeshifter multiple times from different sides. Tom was just taking these attacks, absorbing all of the impacts. When Emolga was finished, he sucked took a deep breath from his gaping mouth. With another attack done, she expected he would counterattack, but she just saw him standing there. Since he wasn’t going to attack, then she went on with her attacks.

Emolga lunged forward at the still non-moving Pokémon at a fast speed that made her look almost invisible. She appeared before Tom and collided with her stomach, damaging him more than he already was. He slides across the ground while taking in the damage from the Quick Attack. His body bloated from swallowing a large quantity of air into his mouth. Before he could grab her, Emolga flew away from him and prepared for her next attack.

“He’s just taking all of those attacks. Why isn’t he attacking?” Pikachu questioned.

“He’s preparing for a stored attack. With all the attacks he’s taken, he must be ready to release an enormous blast.” Shinji spoke, confusing the mouse even more. He didn’t say anything after that, so she decided to watch and see what will happen next.

‘This should finish him.’ Emolga thought. She soars down towards the Victreebell with her tail changing into iron as she was getting closer. This was what Tom wanted.

As the flying electric type was growing closer to him, Tom knew it was finally time to finish this battle. Just as she was growing closer to him, a light blue light formed inside his mouth. It was growing more and more before the light encased the rest of his mouth. Emolga saw this light and was about to turn away, but was too late. The blue light was shot out of Tom’s mouth as a bema of energy, swallowing his opponent in the attack.





The stored attack was too much for Emolga to handle, so she was sent flying. After a minute passed, Tom was finished with his attack. He looked ahead and saw Emolga land on the ground with swirls in her eyes. Seeing she has fainted, Tom took a deep breath, taking this chance to rest after a good battle.

“That wasn’t bad. Using your opponent’s attacks to absorb energy and fire it right back at them. A little too rash for a plan, but not a bad one.” Shinji said, walking up to his exhausted student. Pikachu was walking up to Emolga with a Sitrus Berry in her paw.

“I know, but you said I should focus on one form at a time, so I thought of a way that would deal a lot of damage,” Tom explained.

“Well, it was a good plan nonetheless,” Shinji said before continuing to run through all of his sensei’s drills through the rest of the entire day.

After training for the entire day, Shinji ended it once the sun was setting. He said they would resume tomorrow before he left to rest for the day. With training over, Tom shifted into Keldeo, grabbed his toe electric friends, and headed back home. 

On the way back to the library, he couldn’t stop thinking about his acquired powers. He appreciated them but wasn’t sure why he had them. When he thought about these powers, his mind wondered to his given mission from Arceus.

“What you did back there was incredible, Tom! I’ve never seen any Pokémon do things like that.” Emolga said from his back while munching on an apple.

“Neither have I,” Tom said.

“Could it have anything to do with the mission Arceus gave you,” Pikachu wondered.

“Maybe. The thought did cross my mind,” Tom said.

Emolga’s eyes widened after hearing them mention Arceus. she spat out the apples and crawled up Tom’s neck to look him in the face. She said, “You met Arceus?! The God of all Pokémon? You have to tell me everything.”

Tom sighed and began his story of how he came to Equestria and his mission. The whole time she was listening, she couldn’t believe that he met both Arceus and Mew at the Same time. When she heard that a dark force is coming to the land, she became frightened at the thought whatever it could be. After he was done, she understood how important his mission was and offered her help. He appreciated her want to help and accepted it whenever the time comes.

They finally made it back to the Golden Oaks Library as the moon has risen in the sky. He entered the place and made his way up the stairs so he can get some rest. When walking up the stairs, he caught sight of a light in the room. He made his way to the room and saw Twilight working.

“Twilight?” Tom called the violet mare.

The unicorn heard her name being called and looked behind her. She saw it was Tom who called her name and she smiled. She said, “Oh, Tom. You’ve finally made it back from your training.”

“Yeah, today’s training was a real workout,” He said, walking up to the mare and making a few popping in his neck. “What are you still doing up?”

“I have a few notes I have to write before I go to bed.” Twilight answered.

“Really? Do you want me to stay up to keep you company?” Tom offered.

Twilight thought his offer to stay with her was so kind of him. She said, “That’s so nice, Tom, but I don’t want you to stay awake when you don’t have to be. Besides, I already have to others to stay up with me.”

The mare stepped aside for Tom and his two riders to see two creatures standing on perched. One was an avian Pokémon that resembled an owl with a round body. Most of its feathers were brown, but its belly was cream-colored. It had large, red eyes; a small, pinkish beak; stubby wings; and a fan-like tail with three feathers. Encircling its eyes were black rings; the lower rims of the ring had three protrusions that resemble the teeth on a gear while the upper rims have extensions that resemble the hands of a clock. 





The other was also an owl, but was not a part of the Pokémon species. It was an average owl with dark grayish amber eyes and Pale, light grayish amber feathers. Its also had grayish amber wings, tail, ears and eyebrows.





“This is Owlowiscious and Hopper. They stay up with me as my nighttime assistants so Spike can have a chance to sleep.” Twilight said.

“Wow. That’s pretty clever. And it really nice of them to stay with you while you work. You know one of them is a Pokémon.” Tom said, confusing the mare.

“Really? Which one?” Twilight asked looking at the two owls.

“The owl with the red eyes.” Tom said before he pulled out his phone and aimed it at the Hoothoot.

“Hoothoot, the Owl Pokémon. A Normal and Flying type. It always stands on one foot. It changes feet so fast, the movement can rarely be seen.”

“Incredible. So you really have another foot. I just thought you were the type of owl that had only one foot.” Twilight said, examine the Hoothoot change from one foot to another foot.

“Yeah. Hoothoot are always seen standing one foot.” Tom stated.

“That device is incredible. What is it?” Twilight asked, examining the phone in Tom’s hoof.

“It’s an Arceus Phone. Arceus gave it to me before sending to Equestria. It has all kinds of applications that work similar to phones back where I’m from, including data on all discovered Pokémon and Digimon.” Tom explained.

Twilight was visibly gushing at this new piece of technology. Never in her life has she seen something so compact but with a lot to offer. Hearing that all the information of the new species in her world were on it just made her want it more.

“It has all the information on the creatures? You have to let me see it!” Twilight reached for it with her hooves but Tom pulled it away.

“Uh uh uh. Sorry, Twilight. I still need it to know where I’m going m, but I’ll show it to you soon, okay?” Tom asked.

She pouted in her chair after hearing she couldn’t have the phone at the moment. Tom couldn’t help but find her pouting cute. She asked, “You promise?”

Tom held a hoof to his chest and said, “I promise.”

Twilight could tell he was serious and knew that he was going to keep the promise. With that over, Tom decided it was time to turn in for the night. He walked towards the door and turned around to the still working mare.

“Goodnight, Twilight. Owliwicious. Hopper,” Tom said.

“Goodnight, Tom. Pikachu. Emolga.” Twilight said, bedding the three Pokémon a good night.

“Pikapi.” Pikachu said.

“Emo Emo.” Emolga said.

“Hoo,” Owliwicious hooted.

“Hoot Hoot.” Hopper said.

As all the good nights were out of the way, Tom exited the room and made his way down the hall. He made it to his bedroom and laid down on the bed, with Pikachu and Emolga joining him on opposite sissies of the pillow. One by one, all three of them slowly fell asleep.





The next day quickly followed with the rising of the sun and the sound of Hopper waking everyone up. It came as a surprise to all of them when they woke up to the sound of the living alarm clock. While it wasn’t exactly how they usually woke up, they all decided to just get on with their day.

When they all got up, Spike made breakfast for all of them, while Twilight went on with her series of questions. She asked a few questions about Pokémon before moving onto Digimon. Tom answered the best he could with what knowledge he had about the species. After they were finished with breakfast, Tom decided to head out for today’s training. Pikachu and Emolga stayed behind because Twilight wanted to study the two electric types. With everything packed, Tom took his leave and left the library.

Tom began his walk through the town, earning a few waves from the townsfolk. While waving at them, he couldn’t help but feel bad that no one but his friends knew who he really was. Would the other ponies accept him if they knew he was really human? Would they even like him?

“Are you the one Shinji trains, hmmm?”

A voice pulled him from his train of thoughts and he searched for the owner of that voice. He it came from a Pokémon from the left of him. It was a light blue, bipedal, amphibious Pokémon. Its head was broad and round, having a little neck to distinguish it from the rest of its body. It had a wide mouth and tiny, black eyes. A wavy, purple stripe runs down its back. Along its spine is a dark blue fin, which is large, meaning that it was a male. His hands and feet both have three digits. His outer layer of skin is slimy and slippery.





The sudden appearance of a Quagsire appearing in the middle of town caught Tom completely by surprise. This species was not normally found away from any body of water. He didn’t want to be rude  so he answered, “…Uhhh, yes.”

“Mmm hmm. Good. He asked me to bring you. Would you come with me, hmm?” Quagsire requested.

Tom was unsure why Shinji would ask this Quagsire to bring him when he could come to him so easily. He figured his sensei must have a reason for this, so he just went with. He said, “…Okay.”

“Alright. It’s always better to have a travel buddy, hmm?” Quagsire asked before turning around and walking ahead. Tom followed him right behind the water fish Pokémon.

They have been walking for about a couple of minutes with barely a word from each. Quagsire has just been making small talk the who time and Tom has tried his best to respond back. Once they entered the forest, everything just went quiet, excerpt for Quagsire’s humming.

After a couple of minutes of walking, they finally made it to Tom and Shinji’s usual training area, only Shinji was not there.

“This is it. It sure is refreshingly empty around here, hmm? Well, see ya around, hmm?” Quagsire said before walking back into the forest.

“Wait. Where’s Shinji?” Tom asked. 

“No idea. He just told me to bring you here. Maybe he’ll show later, hmm?” Quagsire said just before he disappeared into the forest.

Tom let out a breath after seeing how he was not very helpful. With no way of knowing when Shinji will get here, he decided just to wait in the area and practice a few moves.





It didn’t seem like a big deal to wait for Shinji, and this gave him the opportunity to practice with his Straw Hat powers. Once the first hour went by, he figured Shinji must be busy with something important. It wasn’t until the second and third hour passed that he was starting to get concerned. This went on until the whole day went by and the moon was up in the sky. Tom was clearly frustrated that his sensei has basically bailed on their training.

“I can’t believe this. He’s the one who told me to come back here for practice but doesn’t even show up.” Tom complained.

Since it didn’t look like Shinji was going to show up anytime soon, Tom decided to call it a day and head back home. While he entered the forest, he missed the pair of glowing, yellow eyes in the bushes just right behind him.

He has been walking through the woods for what felt like an hour while grumbling at his teacher for not showing up. First, he had someone else pick him up for practice, then he wasn’t there when Tom showed up, and finally, he never showed up the entire day. The whole thing was completely ridiculous.

While he was walking in the forest, there was the faint cry in the wind. He stopped in his tracks and searched where that cry came from. He continued to hear the cries before catching sight of something moving in the forest. It was too fast for his eyes to catch but could tell it wasn’t a large creature.

“Hello. Is someone there? Do you need help?” Tom asked the creature rustling in the bushes.

Tom was slowly walking towards the bushes, expecting to find an injured creature. What he didn’t expect to see glowing objects staring him in the eyes. Suddenly, his head was beginning to hurt as everything was getting heavy. He suddenly felt something on his shoulder.

“Hey, buddy. Are you okay?” 

Tom’s eyes widened after hearing a familiar voice behind him. He turned around to find his best friend, Max standing before him.

“Max? What are you doing here?” Tom asked his friend.

“What do you talking about? Of course I’m here. It’s your birthday party.” Max said, waving his arms at all his friends.

Tom couldn’t believe his eyes that right in front of him were all of his friends before he came to Equestria. They were all either conversing with one another or eating the food. He even looked at himself and saw he was a human again.

“How did I get here?” Tom asked his friend. 

“What do you mean? I brought you here just a few minutes ago. Are you okay, man?” Max asked with worry in his voice.

Tom quickly collected himself and said, “Yeah. Sure, man. Everything’s fine.”

“Okay. If anything’s wrong, just tell me. We’re friends right?” Max asked with his fist out.

Tom smiled and hit Max’s fist with his. He said, “Right.”

“Good. Now, good have some punch and enjoy your party.” Max said before walking away.

Tom walked around and greeted the various party goers, asking how they were doing. He soon came across the food and drinks table, and started pouring himself a drink.

‘Was it all just a dream? Did I make everything up. Did I make them up?

“Hey, Tom. You’re never gonna believe who just arrived.” A voice pulled Tom out of his thoughts, which belonged to Max. 

“Oh yeah? Who have showed up-“ Tom said before stopping himself after seeing who was standing behind his best friend.

Behind Max was two adults that looked to be in their fifties: one was an adult man, while the other was an adult female. Tom couldn’t believe that standing in front of him were actually his dead parents. And standing right beside them was someone he never thought he’d ever see never again either: his dead sister.

“Surprise! You’re family came to visit for your party.” Max said.

“Happy birthday, son.” Tom’s dad said.

“Yes. It’s so good to see you.” Tom’s mother said.

Tim’s little sister, Gwen, ran up to him and hugged his waist. She looked up at him and said, “Happy birthday, big brother.”

This whole sight was too much to take. Seeing his dead family standing right in front of him was all that needed to know that everything wasn’t real.

Suddenly, everything around him was becoming distorted. All of the people, the tables, even him was starting got out of phase. Whatever illusion was holding him was starting to come undone and he needed to help it along. He raised his arm and bit down on it hard. This sensation was enough to pull him back to the realm of reality. Soon enough he found himself back in the forest back in his Pokémon form. Now, he needed to find the one who cast that illusion.

“Oh, you’ve come back. Was it not so enjoyable?”

He heard a voice right in front of him. He saw it came from a purple, ghost-like Pokémon. It had a round head with elaborate tufts resembling a witch's hat atop it. The tips of the tufts are paler than most of the body. It has a thin, red mouth that resembles the letter "W." Below its head, it had a long neck with a round lump midway down. Three, elliptical red spheres surround the upper portion of Mismagius's body. There are extensions on the sides of its lower body with the foremost ones tattered compared to rear ones.





“You cast that illusion on me?” Tom asked with rage in his voice.

“Of course. I saw how mad you looked and figured you needed something to ease away the anger. Are you not happy?” Mismagius innocently asked. 

Tom was not happy that this Pokémon has shown him something that he hasn’t faced in a long time. That illusion has pushed him past the point of anger that hasn’t appeared in a long time. 

“No I’m not happy.” Tom said, with a low tone.

“Well, if that’s the case, then I’ll just try again.” Mismagius said as her eyes began glowing again.

Tom knew he had to act fast and began transforming into the first thing he knew that could help. His form changed from Keldeo to Scraggy, a Pokémon that was immune to Psychic moves, like Hypnosis.

Mismagius said that her hypnosis was not working and she looked miffed. She said, “So, it’s true that you can change shape. Oh, well. If my psychic moves won’t work, then I will use others.”

Mismagius spins around and released glowing green leaves from her body. The leaves were hurled at Tom, and he responded by pulling his skin up to block the attack. Once the attack was done, it was Tom’s turn to plan his next move. Fighting type attacks don’t work on Ghost types so he needed something that could have an effect. A few ideas came to mind and he came up with the first one.

Tom  charged forward with his teeth glowing white as he jumped towards the ghost. She merely floated away as he bit down where Mismagius was. He landed on the ground and turned towards the floating Pokémon.

“A dark type move? Smart. But how are you going to hurt me if you can’t catch me?” Mismagius asked while moving around in the sky.

As fast as his eyes could keep up with her, Tom’s movements were too slow to keep up with her. He was so angry at the illusionist for what she’d done could had to push those thoughts away and focus on the task ahead. He closed his eyes and took a deep breath. When his eyes were closed, he could somehow see where she was going to be before she knew it. He could use this to beat her.

“If you’re not gonna fight back, then I will.” Mismagius charged ahead with an Aerial Ace, thinking this will finish him.

When she was just closed enough, Tom opened his eyes, jumped over Mismagius, flipped her, and threw her to the ground. When she smashed into the ground, he reeled his hands back and created a 
ball of black and purple rings of energy. He then combined them and fires the rings as a beam of energy rings. The dark type move created an explosion where Mismagius was, dealing super effective damage.

Tom landed on the ground after dealing two dark type moves and waited for the ghost type to emerge. She soon appeared from the out of the smoke with clear signs of damage and breathing deeply.

“Fine. You don’t want my help, then I’m leaving. But we’ll see each other again. Count on it.” She said before disappearing from sight.

Tom was relieved that the Ghost type was finally gone, and can return back to Ponyville. He returned to his trek through the forest, thinking back to that illusion, and everything in it.

A little ways away from the battle area, there stood Sensei Shinji watching his pupil walk through the forest after seeing him battle Mismagius. Speaking of Mismagius, she suddenly appeared out of thin air next to the trainer. He didn’t seem the least surprised by this.

“So, how was I?” Mismagius asked, clearly proud of her work.

“Adequate.” Shinji blankly said. Mismagius looked upset from his answer.

“Adequate?! Did you see me out there? My illusion was perfect and I battled pretty well out there.” Mismagius boasted.

“That didn’t matter. What mattered was for him to  distinguish reality and illusions. This was a major part of his training for the future.” Shinji said before turning around and walking away.

“You know he’s gonna be mad when he learns about this.” Mismagius said.

Shinji did not stop and said, “I know.”

Mismagius just shrugged her shoulders before disappearing as Shinji never stopped walking.





Off somewhere in Equestria, everything was normal, until a light appeared in the sky. The light grew bigger and bigger until the light was transformed into a portal floating in the air.





This was not a normal portal like the ones the Pokémon and Digimon have come through. It looked like the portal was unstable with the visible cracks around the portal.

From within the portal, a large black claw grabbed the side of the portal just as another claw appeared. The two claws expanded the portal, making it bigger for whatever was on the other side. When the portal was big enough, a pair of dark, wicked eyes appeared in the portal as a large creature was slowly exiting.

“Ahahahahahahahah!”