Pokemon: The Origin of Species by DaystarEld(Pokémon)

Latest Update:January 1st, 2023

Summary: Enter the world of Pokémon from a rational perspective. Instead of starting his journey in ignorance, Red has spent his years studying the creatures so central to his world... and he doesn't quite agree with all the information in his books. No time for rookie mistakes here: he's on a quest to discover the true nature of Pokémon, and maybe even find out where they really come from.

Link: https://www.fanfiction.net/s/9794740/1/Pokemon-The-Origin-of-Species

Word count:1095k

Chapters:112

Chapter 1: Unreliable Predictions

The Verres household's second bedroom looks as though it belongs to two very different people. Or perhaps one person and one rampaging tauros.

The floor is littered with clothes. Used socks lie in unmatched pairs beside shoes, and half the chairs and bedposts have shirts or jackets hanging on them. The walls are completely obscured by maps, charts, and detailed pictures of pokemon biology and life cycles, most with writing scribbled on them in a tight, efficient script. The small cabinet beside the bed is overflowing with books and notepads, some spilled off onto the floor beside it.

Amidst this carnage, certain areas are pristine. Bookshelves line the walls, each filled with textbooks and novels that are all alphabetically organized. The work desk is completely clear of clutter, keyboard and mouse neatly placed an arm's distance from each other. The wires and cables are carefully zip-tied and braced along the wall and desk. A can of sharpened pencils and capped pens sits against the wall, and a notebook rests beside it, open to a crisp, empty white page.

On the bed lies a boy, one leg and arm hanging over its side. On the wall above him there's a calendar opened to June. Most of the boxes in the first half have notes written in them. One by one, X's are drawn through each, right up to the highlighted square in the middle... afterward, the squares of the calendar are blank.

Today's the day after which all earlier predictions cease.

As sunlight slowly fills the room through the drawn shades, a colorful alarm shaped like a chatot suddenly whirs to life. The lid over its round eyes slide open, it raises its head, and its beak yawns wide to emit-

Cacacacacacacacaacacaw!

The boy flails against the covers, sitting up and blinking through gummy eyes. He looks at the time and groans. It's only seven...

Cacacacacacacacaacacaw!

He buries his face in his pillow, right hand taking a second one to cover his head. His left swipes in the direction of the sound, seeking the snooze button but finding only air.

Cacacacacacacacaacacaw!

The boy takes the pillow off his head and swings it down at the alarm. The tip of the pillow brushes the chatot's beak, but the alarm is perched precariously on the end of the nightstand just out of reach. As if whoever decided where to place it had done so after measuring the length of the boy's arm and a pillow.

Cacacacacacacacacacaw!

He bolts back up with a scowl and staggers out of bed just long enough to hit the button and slump back onto the mattress. He sighs as his eyes slip closed-

"Hey Future Red, you awake?"

-and then snap open.

"Remember yet?" the mechanical chatot asks in a young boy's voice. "You predicted having trouble sleeping last night, your last night that is, not mine, and set the alarm to be extra annoying just in case you're unusually tired, since you can't afford to oversleep today."

That... does sound like something he would do, yes. Memories begin to seep through the cobwebs around his mind, and Red lowers the pillow and rubs at the gunk in his eyes so he could look at the calendar.

"Well if you're listening to this you're probably up now, but if not..."

Red scrambles for the alarm, too late-

CACACACACACACACACACACACACA-

Red slams the pillow down on the chatot with a muffled bang that knocks it to the floor, but he's grinning. He remembers now.

Today's the day.

With a rush of energy, Red turns the alarm off properly and sets it back on the dresser, then stumbles to the bathroom to shower, the initial blast of cold water waking him the rest of the way. He brushes his teeth with one hand while washing his hair with the other, then dries up and opens his closet, where his traveling clothes are laid out carefully separate from the rest. Stain resistant, reinforced thread with protective mesh underwire, form fitting but light enough not to hamper movement. He pulls on the black shirt, red and white jacket, and denim pants, then opens the box of new, but broken-in, hiking shoes.

Only after he's fully clothed does he permit himself to look at the clock, which reads...

7:32 AM.

Red slumps. The lab doesn't open until eight. He checks his phone and sees no messages or missed calls.

Foot tapping with impatient energy, he decides to make breakfast to burn a half hour. He goes downstairs to the kitchen and begins preparing food. When the eggs start sizzling he hears his mom's door open upstairs, and then feet treading down to join him.

"Morning Red."

"Morning mom!"

She kisses his head and goes to the fridge. "Your alarm was unusually insistent today."

Red grins. "Yeah, sorry. I set some failsafes."

"Mhmm." She pulls some milk out of the fridge, a winking cartoon miltank on the cover. "Any word from Blue or Professor Oak?"

"No." Red slides some bread into the toaster, then turns the stove off and lifts the eggs onto a plate. When he asked his mother to teach him how to cook last year it was harder to reach the stove without standing on a stepping stool, but now he feels comfortable in the kitchen. A year ago he and Blue spent an afternoon imagining all the worst situations they might find themselves in on their journey, and while most weren't particularly likely or easy to prepare for, the thought of losing all their food while in the wilderness led to them asking Red's mom to teach them how to cook. "He said he would call when it's ready."

"Good then, at least we'll have the morning together." She smiles.

Red was actually thinking of bolting down his breakfast and heading to Blue's for last minute coordination, but he shoves down his impatience and smiles back at her. His mother did her best to hide her worry over the past year, but he saw it all the same. Overly affectionate words, prolonged hugs, and above all, a haunted gaze he only ever picked up in his periphery, when she thought he was too absorbed in his work to notice.

He knew at those moments she was thinking of his father, and worrying that she would lose him too.

So he sets the table and puts out their breakfast, then eats with deliberate slowness. They make small talk, while under the table Red's foot bounces, bounces, bounces, and his gaze flicks to the clock again and again to track the glacial sweep of its hands.

He's buttering his third piece of toast when the house phone rings, and he surges out of his chair with a shout of "I'llgetit!" as he runs to the wall mount. His heart leaps as he sees the lab's public number on the ID.

"Hello!"

"Er... hi?" The man on phone seems startled, and Red takes a deep breath to calm himself. "Is this the Verres residence?"

"Yes." Red says, speaking slowly as iron bands tighten around his chest. "This—is—Red. How—may—I—help—you?"

"Oh, good morning Red, I didn't recognize you there. Professor Oak would like you to come down at your earliest conven-"

"I'monmyway!" Red slams the phone onto its cradle. "It's ready!" he yells to his mom as he runs upstairs, food forgotten.

On top of his dresser sits a large backpack, stuffed with everything from clothing to snackbars, carefully weighed to ensure he could jog with it at length without tiring. He had packed and repacked it the night before in preparation, but after having trouble sleeping he pulled the Kanto map out to study by lamp light, then a list of species types, then a half a dozen other things, until inevitably half the bag's smaller side pockets were spread over his nightstand.

He quickly repacks everything, then slings it over his shoulder and goes to the door. He stops halfway out and looks back.

Red examines his books, his video games, his old toys, knowing it might be months at least before he sees any of it again. His gaze falls on his calendar, with all its empty squares ahead.

Red smiles and closes the door firmly behind him.

His mom is standing by the front door when he goes downstairs. He slows and stands before her, only having to lift his chin a little to meet her gaze.

"Got everything?"

There's a slight hitch to her throat, there then gone, and suddenly Red's throat feels clogged. Don't cry...

"I-I think so."

"You'll call when you get to Viridian?"

"Of course."

"And every night after!"

Red shifts his weight. "Yeah."

"If you need anymore underwear-"

"Mom!" He puts his hand on the doorknob, and she covers it with hers.

"Forgetting something?" She pulls his hat off the wall hook behind her and fits it snug over his dark hair. "There. Now you look ready for anything."

Red tugs the cap's crimson bill a bit lower. "Thanks, I thought it was in my bag."

He reaches for the door again, pauses, and then he hugs her nearly as tight as she hugs him.

"Be careful, Red," she whispers.

"I will, mom."

By the time he reaches Pallet Town's main street, Red's eyes are mostly dry, and he's walking with eager anticipation. The Pallet Lab becomes visible soon after, and upon turning onto its avenue he sees a familiar figure in a dark blue shirt and khakis on the other side of the street.

"Blue!" He waits for a car to pass and jogs across to join his childhood friend, whose own backpack bulges with its contents. "What are you doing here? I thought you'd already be at the lab with your grandpa."

"Nah, just woke up when they called." Blue Oak yawns, rubbing one eye. "Couldn't sleep last night, ended up watching League matches and working on my type chart till after midnight."

Red suppresses a sigh, knowing he's not in a position to throw stones and accustomed by now to his friend's obsession with pokemon battles... an obsession that's divided them more and more in the two years since Professor Oak noticed Red reading books far beyond his grade level, and talked his mother into pulling him from school to apprentice at Pallet Labs.

At first Red thought the growing distance between them was from jealousy on Blue's part, but his friend showed little interest in the scientific pursuits his grandfather and Red shared. It blew Red's mind when a researcher in Johto discovered that, despite pokemon mothers only ever giving birth to their own specie even when mating with a different one, their children sometimes demonstrate powers unique to their father's, proving that some genetic transfer does occur despite no other signs of hybridization. When he explained it to Blue, however, his friend wasn't interested in the implications that pokemon gain intuitive understanding of any abilities they genetically acquire; instead Blue just began feverishly mapping out potential ability combinations to try for breeding competitive pokemon.

Worse than their drift in interests is Red's growing suspicion that the entire concept of pokemon "types," the bedrock upon which all pokemon battle strategy is built, is majorly flawed...

"Let me see?"

Blue pulls out a square of folded paper and hands it to him. Red opens it and examines the hand-made grid.

On the top, from left to right, are seventeen color coded "types." The same types are listed on the left from top to bottom, and where the various types intersect with eachother are X's or checks, though most spaces are empty, and many have the smudges of erased marks. Most of them seem right, though Red doesn't follow the competitive scene enough to tell what changes to the meta are new or outdated.

One change makes him curious. "What's this?" Red points to the erased checkmark where Poison meets Grass. "You removed Plant's weakness to Poison?"

"Yeah. I was watching matchups in the Indigo regionals, and started going back over a lot of the high profile matches. In most cases, Grass pokemon were able to hold their own."

"Huh. Were you just looking at Indigo matches?"

"That's where I'll be competing, so yeah."

Red scratches his hair beneath his cap. "Then your sample size might not have been big enough. Most of the Plant pokemon in Kanto that are competitive have adapted to become poisonous to survive better."

"Well, that's good enough for me."

Red frowns. "What if you come across a non-poisonous Plant type from another region?"

Blue shakes his head. "Theory versus practice, my friend. Doesn't matter if a thousand Grass pokemon would lose to a thousand Poison, if the ones I'm going to be fighting with are exceptions. Besides, I can recognize all the natives anyway."

"Well if it's for more than quick reference it should be accurate to the rule, not the exceptions." Red takes a pencil from his pocket. "Here, just put the checkmark back with an asterisk-"

Blue grabs the paper from him and stuffs it back in his pocket. "Look, you do things your way, I'll do things mine, alright?"

Red rolls his eyes. Thankfully Blue is smart enough to know the difference between anecdotal evidence and evidence from rigorous experimentation, but he still puts too much stock in observation vs theory. Sometimes all it takes is one carefully constructed and repeatable experiment to understand the truth behind a thousand different disputing observations.

They've argued about it often, but last month things came to a head when Blue declared that he'd rather learn from experience than trust what's in books, and that Red would waste his life reading rather than doing anything worth writing about. Red responded that maybe Blue was just too stupid to learn something until he had it beaten into him, and shortly after that one of them had thrown the first punch.

They didn't speak to each other for two weeks after Red's mom pulled them apart, which was about how long it took for his black eye (left to heal without medicine as punishment) to fade. It was only their coming adventure that put their fight behind them by unspoken consent, and Red doesn't want to risk ruining this special day by rehashing it.

Instead they cross a few more streets in silence, until the lab is just a block away and Red's excitement returns. "Still no clue what we'll get?"

"No, he's really sticking to it being a 'surprise,' which has not been helpful for planning. You weren't able to find any hints?"

Red shakes his head. "I really only deal with papers and reports... once in awhile I see some pokemon we're experimenting with, but no records of all the ones there, and I rarely go to the ranch."

They reach the plaza in front of the multistory lab. The building is white and silver and glass, easily the biggest in Pallet Town, and it never fails to impress upon Red how lucky he is to be working at the hub of Pokemon research in Kanto. When Professor Oak moved to Pallet Town to set the lab up, it almost literally put the place on the map. Red's mother told him that by the time he and Blue were born, the town had grown twice as large as it was originally, and in the eleven years since then Red has seen it grow twice as large again.

They enter the air conditioned lab and walk together through the entrance hall, where sketches and diagrams of pokemon physiology are displayed along the walls. Red spots his favorite, a drawing of a dissected bulbasaur that's hundreds of years old. The frail, carefully sealed parchment details how the plant material is rooted and merged with the reptilian body. It's the first historical evidence of someone attempting a naturalistic study of pokemon, rather than the ubiquitous regard of them as supernatural and mythic creatures.

It took a hundred generations for the rest of civilization to catch up with the unknown researcher's perspective. To treat pokemon as creatures that could be studied and understood, rather than just tamed by warriors and warlords seeking to keep their villages safe and expand their territory. A new perspective most honored by those like Samuel Oak, among the first generation of trainers dubbed "Pokemon Professor."

Red and Blue enter the office space and begin to pass a number of scientists that they wave to. Most of them are in their twenties or thirties, and smile at the sight of the youngsters, knowing what they're here for.

"Good luck, Blue!"

"Have fun you two!"

"Red! Come see me after, I've got something for you-"

The two adolescents grin and wave as they walk through the labs, mutually picking up the pace as each other's excitement reignites their own. They're practically jogging by the time they reach the main lab, an open, round room filled with desks and computers, with various scientists scattered around it in groups, and many doors leading off to the smaller areas.

"Good morning!" booms a voice at the center of the room.

Professor Oak stands beside a table, pokedex in one hand and a pokeball in the other. While he spends most of his days indoors now, the old man's skin still holds a hint of the tan he carried most of his life, and though his hair is more silver than gray, his eyes sparkle with undiminished vitality and curiosity. His open white lab coat is heavy with various tools and electronic devices sticking out of its pockets.

"Hey gramps!"

"Morning Professor Oak!"

They run up to him as he puts the pokeball down and slips the pokedex into a pocket. Red can see three pokeballs on the table, each with a colored symbol above the button: a green leaf, an orange flame, and a blue water drop. His foot begins to tap in place again as excitement fills his chest and limbs with energy.

Professor Oak beams at them. "You guys look great. Filled with eagerness and prepared for anything. It almost makes me want to leave this all behind and come along. If I were ten years younger..." He sighs, and claps his hands together. "Well. Time to pass on the torch. But first, an introduction. Leaf?"

A foreign girl with long brown hair stands up from the computer she was sitting at. Red was so focused on the pokeballs he didn't even notice her. She's about his and Blue's age, and seems similarly prepared for travel.

As she approaches, Red looks at the three pokeballs again and blinks. "You're coming with us?"

She smiles. "Nice to meet you."

"Leaf, this is my grandson Blue, and one of my students, Red. Boys, this is Leaf Juniper. She's the granddaughter of an old friend of mine from Unova, and she recently came here to study Kanto pokemon."

Red stares until Blue greets her, then mumbles his own after. He knows of Professor Juniper, of course, and that he has a daughter, Aurea, who also recently became a Professor, but he didn't know he had a granddaughter. He never met someone from Unova before, and he hadn't expected to be setting out with anyone but Blue...

"I thought you only finished making two new prototypes, professor?" Red asks. He knows it's childish, but he doesn't want to have to share his.

"I have. Leaf's mother made her own pokedex based on my last design, so she's trying to expand its listing for their international index."

Professor Oak reaches into his white coat and pulls out two red, slim computers. Red takes his reverently and opens the cover. A pair of touch screens greet him, one a home screen with a bunch of apps, the other a greyed out index of all known pokemon. The list calls to him, just begging to be filled with information.

"My latest design prototype, almost ready for mass production. I want you two to give it a field test by catching as many Pokemon as you can to add to our database. And here are the pokemon you'll be using to start." Oak gestures to the three red and white spheres. "It took me awhile, but I got a hold of a bulbasaur, squirtle, and charmander from the breeders."

Yes! Red barely stops himself from pumping a fist into the air, and Blue cracks his knuckles in anticipation. Such rare and strong starting pokemon had been almost beyond his hopes.

"They've been bred and raised to be among the most intelligent and obedient of their species, which will make training them easier than most wild pokemon you catch." Professor Oak says as he picks up the leaf-imprinted pokeball. "Treat them well, train them properly, and they'll be your friends and protectors until their last breath."

The professor holds the lens button on its front level with the lens on the front of Red's pokedex, and to his delight a bulbasaur suddenly appears on the main screen, sleeping in the simulated environment the pokeball creates for him: a lush, grassy clearing in the middle of a forest. Its name pops up at the top of the screen, and after a second of loading, Red sees the Pokemon's vital stats get listed: height, weight, type, and more.

Professor Oak moves the ball away from Red's pokedex and does the same thing to Blue's and Leaf's. The video on Red's pokedex freezes as soon as the lens is no longer aligned, and #001 fills and colors Bulbasaur's name in green and purple.

"When you catch a new Pokemon, just hold it up to the lens like this, and the pokedex will identify it and record whatever information it can. Your pokedexes all have access to the sum total of knowledge we currently have about the various species, and it's up to you to catch as many pokemon as possible to help us gather new information on them. The more you catch, even among the same species, the more data we have on them, so each capture you make has the potential to teach us more. Do your best to try to catch them all!"

Heart in his throat, Red begins to look over all the information the pokedex has on bulbasaur:

Bulbasaur: Seed Pokemon. It exists in a symbiotic relationship with a seed embedded in its back at birth, which sprouts and grows as it ages. The plant absorbs nutrients from bulbasaur's body, while bulbasaur can photosynthesize light through the plant's leaves. It can go for days without eating as long as it has enough sunlight and water, and the plant can survive without sunlight as long as bulbasaur can find food.

It goes on for several pages to describe all that has been learned about bulbasaur's growth, mating habits, preferred environments, and more. After the professor finishes scanning bulbasaur to each of their pokedex, he does the same thing with charmander and squirtle.

"So, I'm going to give you all time to examine these pokemon, then you'll get to choose which one you want."

Red exchanges a look with Blue and Leaf. The Unovan smiles and gestures to the two boys.

"After you: I'm a guest here, and they're all new to me anyway. I have no preference."

"What about you, Red?" Blue asked. "Got a favorite?"

Red can only remember a handful of details about the rare pokemon, and looks at the most recent entry:

Squirtle: Turtle Pokemon. Its shell is hard and smooth, providing great defense and allowing swift swimming beneath the water. Its skin absorbs moisture from the air to fill its water pouches, and when threatened, it can withdraw into its shell and shoot foam or water from its mouth in a powerful spray. It also has strong jaws for biting anything that gets too near.

A pretty straightforward water type, then. He moves on to:

Charmander: Lizard Pokemon. Charmander prefer rocky, mountainous terrain, and hatch from their eggs when their tails ignite and crack the shell. The flame on the end of their tail varies in strength and size based on their mood and health. It is said that Charmander dies if its flame goes out.

Red frowns. It is said? "Professor, this entry on charmander... it says that it dies if the flame on the end of its tail goes out. That can't be right, can it?"

Professor Oak shrugs. "Based on what's been observed, that's the inference many have drawn."

Hmm. The Professor had worded that rather oddly. "But if the flame varies based on their health, wouldn't it be more logical to say that when they die, the fire goes out?"

"More logical?" Blue says. "Who cares if it sounds more logical? He just said that it's been observed."

"But that's a fallacy of correlation and causation," Red says. "Just because the two things happen at the same time, doesn't mean one causes the other, or that we can tell which one causes which."

Leaf surprises Red by nodding. "It's like saying 'Pidove flock in city parks because people there feed them.' But pidove might be there anyway even if no one feeds them, because the parks are where the insects and berries they would normally eat are. So maybe people feed pidove in the parks because they like feeding pidove, and that's where pidove happen to be because of the environment."

Professor Oak examines the image of the charmander sleeping in its artificial cave, tail flame lighting its surroundings. "Well, charmander won't go anywhere near water in quantities larger than a puddle, so short of forcing one to submerge, there's just no way to tell for sure... and since that might kill the charmander, we obviously wouldn't try that experiment."

"Of course not, but... there has to be some other way of determining it." Red picks up the charmander's pokeball. Here's a worthy first mystery to take on: he would find a way to prove one way or the other how charmander's fire relates to their vitality, and begin earning his Pokemon Researcher license. "I've decided. If it's okay with the other two, I want to study charmander."

As Red suspected, Blue immediately picks up the Water type. "I choose squirtle." He grins and spins the pokeball around on the tip of his finger before tossing it up a bit and catching it. Red wonders how long Blue practiced that. Either way it looks cool, and he has to stop himself from attempting it himself. He'll try later in private.

"Well, I guess that leaves me with bulbasaur," Leaf says happily as she picks it up. "I was lying earlier when I said I had no favorite. It has a certain symmetry, don't you think?"

"It does indeed," Professor Oak says with a smile. He reaches into his pocket and pulls out a velvet bag, then carefully pours a handful of shrunken pokeballs into his palm and hands them out. "Press the button to expand or shrink its size. When you catch a new Pokemon, it will be atomized and compressed inside it, but you won't be able to shrink it again. If you have too many to carry around comfortably, you can store your pokemon at any computer connected to the network, and withdraw them from a different one later."

"Is the pokemon's data kept in the ball?" Red asks.

"No, it transfers with the pokemon to the network." Professor Oak points to the computer hard drive at the nearest PC. "That pokeball will still be programmed for it though, so best to hold onto it." He hands out pamphlets that detail the pokeball's functions, and another for the pokedex. "The balls are capable of basic verbal commands to release, withdraw, and nickname your pokemon, but the pokedex is how you interface with the pokemon themselves for virtual training while they're in their balls."

"So if we lose these balls or something happens to them, our pokemon are safe." Leaf says.

"For the ones you have stored, yes, though it's a hassle to get it rekeyed to another pokeball: you essentially have to release it and catch it again."

Red examines his pokeball. He learned all this in bits and pieces over the months of working here, but it still fascinates him how amazing technology has become. He remembers seeing a picture of pokeball technology back when Professor Oak was his age, before there was an internet to rapidly transmit the pokemon from one place to another, let alone allow the balls to change their size. It looked like a big metal coconut.

"I know how eager you all are to get on your way, so let's get your accounts set up," Professor Oak says.

They walk to the nearest PC, and Blue smiles at Red. "So, care to try a battle when we leave? You know, as an 'experiment,' to see if the type charts are accurate."

Red sighs. "I never said they're all wrong... I know Water types are strong against Fire."

Leaf looks at them curiously. "Was that ever in doubt?"

Blue puts his hand on Red's shoulder. "Our Red thinks he knows better than everyone else how pokemon really work."

Red shrugs off Blue's hand. "I think the 'typing' method that all the battle trainers are obsessed over has problems, that's all."

"And he thinks this based on his many years of first-hand training and battling experience," Blue confides to Leaf, who giggles.

Red feels his cheeks flush, but Professor Oak speaks up from the front of the group. "Red may very well be right about some of his ideas: no Professor I've met has claimed to be a hundred percent sure they understand how pokemon work. They're mysterious creatures, and we've only recently had the technology to really study them thoroughly and scientifically."

Leaf nods. "Mom is always talking about how often she gets something wrong before she gets it right. So are you journeying to become a Professor, Red?"

"For now I'd be satisfied with getting my Researcher license and filling the Kanto pokedex." They arrive at the PC, and Professor Oak begins setting up their accounts. "But yeah, I'm going to become a Professor eventually and get my own lab."

"Really?" Leaf looks interested rather than skeptical, which is a nice change of pace. Most people outside the lab don't tend to take him seriously. But then, she is the granddaughter and daughter of Professors herself. "What will your lab focus on?"

"I want to study the origin of pokemon species."

"Which ones?"

"All of them."

Now she looks skeptical. "All of them? You mean..."

Red tries to ignore Blue's smirk. "Yeah. I want to know where they all came from. What makes them so different from each other, and what makes us so different from them."

The girl gives a low whistle. "You and the rest of the world. You don't dream small, do you?"

Red smiles. "Where's the fun in that?"

"None at all," Professor Oak says as he registers Blue's Trainer ID to the network.

Leaf smiles back. "Well, I'll be happy to hear about your theories on pokemon types sometime."

"And I'll be happy to help prove them wrong," Blue says with a grin, and spins his pokeball on a finger again. "Through battles."

Link: https://www.fanfiction.net/s/9794740/1/Pokemon-The-Origin-of-Species