A/N: This came about as I was reading one of the many Pokémon/Portal crossovers. I disagreed, as usual, with their choice of Pokémon for each of the characters and started thinking about what Pokémon I would make them. This lead to me thinking up a story as an excuse to show what Pokémon I think each of the Portal characters should be. I will explain my reasoning for each character at the end of a chapter in which new characters are introduced. If you have any objections or want to share your own reasoning, feel free to review, I'm curious to see how other people match characters to Pokémon.

This fanfiction is going to take place in a Mystery Dungeon universe, probably a conglomeration of Red/Blue Rescue Team and Explorers of Time/Darkness plus some made-up stuff to accommodate later generations. Also, I have all of the Pokémon in this fic, nicknamed and everything, in Alpha Sapphire as a way to simulate what's going on so I know how strong they will be at certain levels and how quickly they will level up.

Edit: Thunderous River is now to the west of town. That's it. No need to reread it.

Something was very, very wrong. As GLaDOS's mind slowly crept back into consciousness, she realized to what extent how wrong things were. She was completely disconnected from her chassis and lying on some sort of floor. Her thoughts, rather than being neatly packed into files, were now fluid and mixed together. Am I… organic? Did someone transfer me into a human body? She wondered as panic began to rise inside her. She tried to move. She tried to turn on her optic or open her eyes or whatever she had in terms of vision.

Opening a single eye, she could see small amounts of light filtering through a thick canopy leaves above her through blades of long grass. She was in a forest, she realized, with the circuit-chilling sound of birds ringing overhead. Gathering her strength, and fighting down what she figured must be nausea, she lifted herself up and assessed the situation.

GLaDOS could tell she had been turned into something organic – she was breathing, in a way, and her brain was in no way a computer – and yet she still felt somewhat mechanical. She had no limbs, and was apparently levitating without even thinking about it. Her spherical head was set in a ball-and-socket joint at the end of her long, vaguely cylindrical body, allowing her to look in every direction except behind herself and straight up due to some sort of crest above her head, and she seemed to be covered in dark blue-gray metal.

Since she could levitate, she wondered if she could fly, since getting above the trees could help her figure out where to go. She forced herself higher, noting that floating higher cost more energy. She lowered herself again to comfortable level that wasn't difficult to maintain but was higher than the grass and looked around. She was in a forest clearing, with thick underbrush and trees on either side with a pathway extending to the side. The thorny bushes and spikey trunks formed a wall of wood, thorns, and leaves that seemed too thick to push through and too high to levitate over without a great deal of effort. The pathway was also surrounded, making it essentially a dark corridor.

She pushed herself forward, entering the corridor as she searched the soup that was left her mind to try to figure out what happened. The last thing she clearly remembered was testing Orange and Blue, but after that… nothing. She vaguely remembered pain and light, but for the most part it was like everything faded before she woke up here, in a strange new body in the middle of the wilderness. Maybe some sort of portal device malfunctioned; after all, a myriad of problems had occurred with the Perpetual Testing Initiative all those years ago, including employees and equipment suddenly going missing. Unfortunately, the scientists had never found a way to bring all those people or machinery back.

As the corridor opened into another clearing, again surrounded by thick foliage, GLaDOS heard a soft, high-pitched growl. A rat-like creature with purple fur was glaring at her, whiskers twitching, baring its large fangs. With a squeak, it lunged at her, bashing its little face against her side.

Rattata used Tackle! It's not very effective…

A small amount of pain flared from the impact, but barely bothered her. The rat backed up, preparing for another lunge. GLaDOS knew she wasn't fast enough to flee, and while it didn't hurt much, it would certainly be annoying to have this thing follow her around, bashing its face against her. Her only weapon was her own face, but the difference was that she was made of metal.

GLaDOS used Take Down! GLaDOS is damaged by the recoil!

Attacking the rat hurt worse than getting attacked by it. Luckily, it was enough. The animal was knocked backward and slid along the ground unceremoniously. Getting up and shaking itself, it turned and fled. The pain from the battle slowly ebbed as GLaDOS pressed on through the forest.

After traveling for a while, she found a clearing with clear pond and decided to check her reflection. A single, golden eye stared back at her through the rippling water, much like her real body, except it was attached to a small, levitating cylinder of metal rather than the large, impressive chassis she was used to. The creature she had become was nothing like anything ever documented by science, at least not in the universe she was from. It was likely that this was one of the parallel universes discovered during the doomed-to-fail Perpetual Testing Initiative, which resulted in many interesting worlds being found. Out of curiosity, she lightly touched the surface of the water. She could feel the cool wetness, a little, at least. She noticed that she lacked any sort of mouth and was wondering if she needed to drink when she heard the scream of a bitterly familiar voice followed by a loud splash.

"Oh, for God's- a dead end!" the accented voice, surprisingly, came from a reddish-orange fish that had just fallen into the pond from a small waterfall that fed into it at the opposite end. The fish hovered at the surface, glaring at the short waterfall. "It's bad enough that I couldn't fight the current, but at least I was going somewhere. Now what?" He turned and spotted GLaDOS. "Oh. Hello!" he called, clearly not recognizing her as he tried to wave with his fin only to flop onto his side in the water.

GLaDOS sighed. "Of all the people I could have run into, of course I run into the dumbest moron who ever lived, who nearly destroyed my entire facility."

What had appeared to be a grin on Wheatley's face quickly disappeared. "Oh. And of course I had to run into you, the… the…"

"Most intelligent, advanced AI ever created?"

"NO! I mean, well, yes, but you are also the, um, the… most… mean, yeah, the meanest AI ever created!" the fish shot back.

"I would think that betraying and attempting to kill the one and only person who ever helped you and possibly even liked you was a rather mean thing to do. Not to mention stuffing me into a potato. Thanks for that, by the way," she responded coldly.

"Oh, yeah? Well, I… You…"

"You know what? You're wasting my time. I need to figure out a way to get to my facility, and you are obviously nothing but a diversion." She turned to leave and began levitating away.

"W-wait!" Wheatley called, leaping out of the water and flopping onto the grass.

GLaDOS gave him a sideways glance. "Don't you need water to breath, considering that you were turned into a fish?"

"Um, maybe? I mean, it's more comfortable in the water, but I guess I'm not suffocating right now…"

"I suppose the Perpetual Testing Initiative discovered universes where our own laws of science didn't apply; this one is probably no different," she concluded, turning to leave again.

"Wait, let me come with you!" he called, flopping after her.

"Why would I ever allow you to come with me?" she demanded, whirling around to glare at him.

"Um, I could, uh, help with… water! Yeah, if you ever, you know, have ponds that need investigating, or, or what if you fell in? Huh? Can you swim? It doesn't look like you can swim," he replied.

"One, I can levitate over water, and two, I don't see why I would ever need to investigate a pond."

"Oh, come on! We're from the same world, right? Shouldn't we stick together to find a way back?" he protested.

"How could you possibly help me? You're a fish that's so weak it can't even swim upstream, which is amazingly fitting for you, by the way," she retorted.

"What if I-" He was interrupted by a loud shriek from one of the pathways leading out of the clearing.

Meanwhile…

"No, wait! You have to take us back!" the young male Starly pleaded.

"Sorry, chick," the female Jolteon replied, "Rescue teams don't operate for free."

"B-but," the female Starly protested, "When you said you would help find my brother, you didn't mention payment!"

"You should have known," the Sneasel, also female, chided, "It's not a mystery that hiring a rescue team can be expensive, especially top-notch rescue teams like Team Quickstep."

The two Pokémon turned to leave.

The male Starly gathered his courage. "Oh, yeah?" he finally called after them, "If you don't take us out of this Dungeon, we'll just follow you!"

The Jolteon and the Sneasel froze, and the Starly swallowed hard as they turned to face him.

"Not if we make you faint!" threatened the Sneasel, spreading the two large claws on her paw at him. The Jolteon growled in agreement, tiny sparks crackling along her yellow flank.

Chell, watching from the shadows of the corridor outside the clearing, decided she didn't like where this was going. She had been thrown into a strange world, turned into a strange blue dinosaur thing, and found it rather strange that she could understand the speech of other species of strange animals while still being unable to speak herself, but still felt like someone needed to help those two young birds. They didn't look like they were any match for the black cat-weasel hybrid creature or the yellow fox that threatened them. Chell didn't know if she would be much better at fighting, but what she did know was that in this form she had a large, hard head with a nasty bite and little bit of fire that the creatures that tried to attack her before didn't seem to like.

She stepped into the corridor and tried to clear her throat to catch the creature's attention, but instead of "ahem" it came out as a growl. The cat-weasel and the fox turned.

"What's a Bagon doing out in this forest? Are you in a rescue team, too?" the fox asked.

Unable to reply verbally, Chell walked around the two animals and stood in front of the birds, facing the cat-weasel and the fox.

"Wow! Is she helping us?" the male bird asked his sister excitedly.

"Well, are you? Speak up! Meowth got your tongue?" the fox demanded.

Chell silently nodded.

"Oh, yeah? Well…" The cat-weasel challenged. She paused, as if trying to think of something cool to say. "Well, we'll teach you not to mess with Team Quickstep!"

The creature charged, her long claws glinting in the sunlight. Chell lowered her head and charged as well.

What happened next was rather like what would happen if a cowboy tried to beat a bull at his own game. Chell, with her hard head, felt the impact much less than the cat-weasel, who was sent flying, shrieking until she hit the ground with a thud.

"You… you stupid little dragon!" the fox snarled, sparking even more.

I'm a dragon? Chell thought.

It was at this point that, after hearing the cat-weasel shriek, GLaDOS levitated into the clearing, followed by Wheatley who was awkwardly flopping along on the forest floor.

"What is going on here?" she asked, curious.

Chell looked at the odd metallic creature, recognizing her voice.

"What's going on?!" yelled the cat-weasel as she got up, "Here we are in the middle of a rescue mission, and this Bagon waltzes in here and attacks us without saying a word!"

"But you weren't rescuing us!" the female bird yelped.

"Oh, no," GLaDOS sighed, fixating her gaze on what was apparently a Bagon, "It's you, isn't?"

Chell nodded silently.

"It's who?" Wheatley asked

"Her," GLaDOS replied.

"Who?" asked the fox.

"Oh God, it's her?" Wheatley said, astonished.

"Who is she?" demanded the cat-weasel.

"The lady!" Wheatley replied.

"The what?" asked the cat-weasel.

"The 'Bagon'," GLaDOS corrected.

"But who is she?" asked the fox, very confused by this point.

GLaDOS rolled her eye. "Her name is Chell," she finally explained.

"Nice to meet you, Chell," said the male bird. She nodded in acknowledgment.

"You know her?" the fox asked GLaDOS.

"Unfortunately," the former AI replied.

"Anyway," exclaimed the cat-weasel, "Are we going to go back to fighting, or what?"

"We're fighting?" Wheatley yelped, alarmed.

"Not you, stupid Magikarp," the cat-weasel scoffed, "The Pokémon who can actually fight."

"If you're with her," the fox growled at GLaDOS, "Then you're against us, too!"

"What? I'm not with – Hey!"

Jolteon used Tackle! It's not very effective…

"That barely hurt, you know," GLaDOS taunted, though did hurt significantly more than a little mouse bashing its face into her steel hide.

Meanwhile, Chell was again facing off against the cat-weasel, who now knew not to charge at her.

Chell used Ember! It's super effective!

Sneasel used Scratch!

Wheatley used Splash! But nothing happened!

"What are you doing, moron?" GLaDOS asked.

"Umm…" Wheatley began. He was interrupted by the fox again attacking GLaDOS.

"Are you really going to keep doing that? I'm made of metal. I'm surprised that doesn't hurt you more than it hurts me. I'm getting sick of it, though." GLaDOS had been resisting using her actual move and had resorted to lighter attacks, knowing the recoil damage would add up. However, she was getting tired of the relentless tackles.

GLaDOS used Take Down! GLaDOS is damaged by the recoil!

The fox was sent skidding back. "Ow ow ow…" she muttered, "That stings…"

"Are you going to attack again, after that?" GLaDOS inquired tauntingly.

The fox steadied herself and charged.

Jolteon used Tackle! GLaDOS avoided the attack!

GLaDOS used Take Down! GLaDOS is damaged by the recoil!

Jolteon used Sand Attack! GLaDOS' stats were not lowered due to Clear Body!

On the other end of the clearing, the cat-weasel had not been having a good time since Chell discovered she was weak to her Ember attack. She had even been burned, which ticked away her strength as the battle wore on.

Sneasel used Scratch!

Chell used Ember! It's super effective!

Sneasel is hurt by her burn!

Sneasel used Leer! Chell's Defense fell!

Chell used Ember! It's super effective!

Sneasel is hurt by her burn!

Wheatley used Splash! But nothing happened!

And on it went until finally the two Pokémon gave up.

"Enough, enough…"the fox sighed, limping up to her cat-weasel friend, "We're leaving, okay?"

"Don't think this is over," the cat-weasel warned, "Team Quickstep will get you back, you just wait!"

The Jolteon and the Sneasel fled!

GLaDOS grew to Lv. 6!

Chell grew to Lv. 6!

Wheatley grew to Lv. 6!

The two birds fluttered up to Chell and GLaDOS fast enough to make GLaDOS jump – or rather, levitate rapidly – back with a start.

"Wow! You guys were great!" the male bird exclaimed, looking at the two of them adoringly as Wheatley flopped up to join them. "By the way, I'm Lee, and this is my sister, Star."

"Are you guys a rescue team? Or an exploration team?" Star asked excitedly.

"No, actually," GLaDOS replied.

"Oh," Lee said, looking disappointed, "Well, you should be one, because you guys were awesome."

"Could you, uh, help us get out of this forest anyway?" Star asked shyly.

"We don't know the way out ourselves," the former AI pointed out.

"No one 'knows' the way out of a Dungeon," Star said, looking confused, "They change all the time, silly! But you're strong enough to fight your way out."

GLaDOS did not appreciate being called 'silly' by a bird.

"Well, uh," Wheatley interjected, making everyone notice he was there lying on his side in the grass for the first time, "we aren't exactly from here, you know."

"Watch what you say, moron," GLaDOS warned.

"What?"

"We don't want to draw attention to ourselves," she explained, knowing it was too late now.

"Oh! Are you from another world?" Lee asked, flapping his little wings with excitement.

"Oh, hush!" his sister said, pecking him, "Those are just stupid stories."

"Actually-" Wheatley began before GLaDOS shot him a glare.

"What do you mean by 'other worlds'?" she asked cautiously.

"There have been rumors," Lee began, "of Pokémon popping up in Dungeons who not only know nothing about Pokémon – like, they don't even know what types are or what species they are – and even claim that they are not Pokémon! They say they're humans!"

"There are no humans around here anymore," Star explained, "But even if there were, they would at least know about Pokémon. They used to catch and train us. But these are just rumors."

"But everyone knows about Dungeons; they're everywhere!" Lee insisted, "If they don't know about Dungeons, they must be from another world! Well? Are you?"

"Yeah," Wheatley replied.

GLaDOS would have preferred to keep the fact that they were from another world a secret since they had no idea how others would react. These two birds, who were obviously quite young, may be fascinated, but others may consider them insane or dangerous.

"That's so cool!" Lee beamed. He pecked his sister. "I told you!"

"But are you really or are you just saying that?" Star inquired suspiciously, cocking her head.

"What world are you from?" Lee asked excitedly, disregarding her.

"Look, it's difficult to explain," GLaDOS replied, "Why don't we get out of this… 'Dungeon' and you can explain a few things about your world."

They wandered on through the Dungeon, which was apparent called "Thorn Woods" after the thorny foliage that formed its walls, with the birds carrying Wheatley. It was apparently one of the smaller and 'easier' dungeons. As they went, Lee rapidly explained practically everything they needed to know about the world of Pokémon, from their species – the two birds were apparently Starly, GLaDOS was a Beldum, Chell was a Bagon, and Wheatley was a Magikarp – to types and type match-ups to stats. Finally, they found a corridor with light on the other end, indicating a way out. Exiting the Dungeon, they entered a normal forest with trees and bushes scattered about rather than massed together in thick walls. From there, the Starly lead the way to the town as night started to fall.

The town was fairly small and was located on the coast with half of it floating over the water. To the west of the town was a beach bordered to its west by cliffs. The half of the town that was on solid ground was made up of small stone buildings while the half over the water was made of wood. The buildings appeared to all be shops, with Pokémon standing in front of counters with the buildings behind them. Nothing, however, looked like a house. The Starly gave them a quick tour, pointing out a shop run by Pokémon called Kecleon, a bank run by a Persian, and a storage building run by Kangaskhan. At the top of the cliff, they said, was the post office, headed by Pelipper.

"If you want to be a rescue team, you'll have to register at the Pelipper Post Office," Lee explained.

"But we don't want to be a rescue team," GLaDOS said for the umpteenth time.

"But you're so – well, since you're only level 6 right now, I can't exactly say strong," Star said, "But you've got potential! Besides, you need to make money somehow, and if you really are from another world, you'll probably have to go into Dungeons to find out how to get home. Rescue teams have the most access to Dungeons."

"And they say," Lee pressed, "That if someone comes here from another world, they pop up in Dungeons, like you did. What if you have friends out there?"

"Trust me, I don't, and I seriously doubt these two do," GLaDOS replied.

"B-but…" Lee protested, searching for words, "but you'll need to go into Dungeons, and you need money… I mean, unless you want to spend the rest of your life as a store clerk like the Kecleon brothers… Not that there's anything wrong with that, but if you want to go home, you'll probably need to find Legendries to help you, and they're in Dungeons…"

"Hmm…" GLaDOS turned her back on them, thinking this over. Wheatley had been unusually quiet, and Chell had been watching her expectantly. The decision was on her, it seemed, which she was fine with.

"Alright," she said finally, "We'll go ahead and register, just in case it becomes necessary, but don't expect too much."

"Awesome!" Lee flew up in the air and did a somersault, leaving his sister to drop Wheatley on the ground. "Now all you need is a team name, and a mailing address – Oh! You don't have a place to stay do you? Um, uh…" Lee looked about frantically, as if a house would suddenly pop out of the ground for him. "Oh! I know of the perfect place! Follow me!" He darted off toward the beach.

He led them to the cliff face at the edge of the beach, where he pulled aside some vines to reveal a cave hidden behind them, complete with a mailbox.

"A rescue team used to live here, but they cleared out," he explained, "I think they even left their beds and chests here."

Inside was a cavern with a few beds made of moldy straw that must have been left there for a while with a few wooded chests next to them. In the middle was a fire pit, and at the far end a couple tunnels extended into darkness. The walls were ringed with unlit torches. Despite being by the beach, this room, at least, was fairly dry. The Starly dropped Wheatley in the ocean, claiming that they thought there was a cave entrance underwater as well.

"I guess you'll have to replace the beds…" Star said, looking concerned. Chell stepped up to one of them, sneezed, and stepped away again.

They went back outside, where Wheatley was floating close to shore.

"Now all you need is a team name," Lee said, "How about team… team… Bag… dum… karp? Because you have a Bagon, a Beldum, and a Magikarp?"

"No," GLaDOS said immediately, "I suppose the one thing we all have in common is Aperture, so we'll just call it that." Chell shrugged in response.

"Team Aperture? Okay, if you say so… We'll go to the Pelipper Post Office for you, so you guys can get settled in," Lee said. With that, the Starly siblings flew up the cliff.

"Wow. What a day, eh?" Wheatley said, "First we get thrown in this strange new world, now we're a rescue team…"

"What do you mean, 'we'?" GLaDOS asked, "What makes you think you're on the team?"

"B-but, I…"

"You can't even walk, let alone defend yourself. It's clear we're going to have to do a lot of fighting, which is hard enough in these strange bodies. We don't need to be looking after you as well. You would only slow us down, not to mention the fact that you've tried to kill us before. Consider this punishment" she explained coldly. She levitated back toward the cave, looking back to make sure her former test subject would follow.

"Chell…" he called softly. Chell looked from him to GLaDOS, then followed her into the cave.

"I guess that's what I get for being all bossy before…" he muttered to himself before turning and swimming out into deeper waters, "But I am not weak or useless or a moron. I'll show them. I'll prove myself, somehow…"

A large blue sea creature with a spikey grey shell (Whom he later found out was a Lapras) swam gracefully toward him. At first he panicked, thinking she was about to eat him, but then she spoke in a soothing voice, "Try swimming upstream."

"What? Oh, sorry, I don't think I have time right now for, uh, wise words of… wisdom," he stammered, turning to swim away.

"I wasn't trying to be wise," she said with a chuckle, "I meant that literally. The Thunderous River empties into the ocean west of the town. Since they are not natural fighters, many Magikarp toughen themselves up by swimming against currents, like that of the river."

"Really?"

"Indeed. Far down the river is a waterfall. They say that if a Magikarp can get to the top of a waterfall, it will evolve into Gyarados, which is a rather powerful Pokémon," she explained.

"All I have to do is swim to the top of the waterfall? Great!" Wheatley swam east toward the town, forgetting his difficulty with the stream earlier that day.

"It's not that easy-" she called after him, but he didn't stop.

Meanwhile, Chell and GLaDOS tried to settle into their new home. Chell lit the torches with her Ember attack, then went outside for firewood.

With a fire lit in the center of the cavern, they sat in awkward silence. GLaDOS found that she could cling to the rock wall using the hooks on her backside, which seemed like a comfortable enough way to sleep. Chell had apparently decided that the stone floor by the fire was better than the moldy straw beds, which was probably for the best. The last thing either of them needed was for one of them to get sick.

As if through some silent agreement, they decided to go to sleep.

A/N: First of all, allow me to explain why I have Chell as a Salamence (I focused on the final evolutions, since that's what they'll eventually become). First, when looking for Pokémon for her, I focused on Flying types. There are two reasons. First, in the line "Mia bambina, oh ciel!" from "Cara Mia Addio," the word "ciel" is used as a pun on Chell's name and means "sky" or "heaven." The second and main reason, though, is that wings and flight tend to symbols for freedom, and all she is really doing throughout the game is fighting for freedom. Her tenacity and determination to be free is another reason I chose Salamence. Bagon (and presumably Shelgon) long to fly, and their determination to fly is so strong that it triggers a mutation that allows them to grow wings and become Salamence. Mutating your body by force of will is almost as astonishing as a human test subject not only surviving a journey from the depths of Aperture and back while omnipotent, homicidal AIs try to kill her, but in the end befriending one such omnipotent, homicidal AI.

GLaDOS was a bit easier. When it comes to super-intelligent Pokémon (of course she has to be one of the super-intelligent Pokémon), three come to mind. There's Alakazam, a… bipedal fox that bends spoons? I know it has an IQ of 5,000, but it didn't strike me as fitting. Its abilities are like those of so-called psychics in real life, which have been thoroughly debunked by science, which is another reason I didn't pick it for a science-obsessed AI. Second, there's Slowking. The reason I didn't pick it is obvious; it's pink, squishy, and she would have to start off as one of the stupidest Pokémon and hope that a Shellder bites her head. Then there's Metagross. It's more intelligent than a supercomputer (or at least smarter than a supercomputer in the Pokémon world; in the Portal universe it might be as smart as GLaDOS) and it's robotic, which is nicely fitting. It's also a pseudo-legendary, which correlates to GLaDOS' omnipotent power over Aperture. On a side note, I know the Pokédex says that Metagross results from the fusion of two Metang and Metang results from the fusion of two Beldum, but in the game you don't actually need four Beldum to get a Metagross. A Beldum just evolves into a Metang like any other Pokémon, so that's how it will work here.

Finally, we have Wheatley as a Gyarados. The transition from a weak little Magikarp to a powerful Gyarados with a terrible temper and a reputation for destroying cities seemed reminiscent of Wheatley going from a weak little core to being in charge of the whole facility while also gaining a terrible temper and nearly destroying the facility. I honestly looked into Water types for him because his optic is blue and most people seem to make him a Water type, but it honestly seemed to work out well, not to mention that I wanted all three of them to be able to Mega Evolve.

Note that the other character's Pokémon may not be as fitting since I was also concerned with having a balanced team.