Your punctuation of dialogue is often inconsistent and thus by extension often incorrect, so it sounds like you could use a primer in how it works.
Dialogue tags - things like "he said", "she said, annoyed", "he shouted", etc. - are insertions into a sentence, not sentences of their own. So say you're going to add a dialogue tag to a sentence such as, "My name is Bob." This is done in one of the following ways:
He said, "My name is Bob."
"My name," he said, "is Bob."
"My name is Bob," he said.
Note that wherever a dialogue tag is separated from the actual dialogue, there is a comma; that if there is a comma after a quoted sentence, it goes inside the quotation marks; that the capitalization of the quoted sentence acts as if the dialogue tag simply weren't there; and that the capitalization of the dialogue tags acts as if the quotation marks weren't there. This means all of the following are incorrect:
He said "My name is Bob."
"My name" he said "is Bob."
"My name is Bob" he said.
"My name is Bob." He said.
He said, "my name is Bob."
"My name is Bob", he said.
Also note that if you have a dialogue tag after one quoted sentence and then have another quoted sentence afterwards, that's different from inserting a dialogue tag into the middle of a single quoted sentence. The second quoted sentence is irrelevant to the dialogue tag attached to the first one. So this is correct:
"My name is Bob," he said. "What's yours?"
When the sentence you're quoting ends in something other than a period - such as an exclamation mark, a question mark, or an ellipsis - then you do not replace it with a comma even if it's followed by a dialogue tag,
but the capitalization of the dialogue tag still follows the same rules as usual, like so:
"What is your name?" he asked.
"Hurry up!" she said. "We're getting late!"
"I don't know..." he said hesitantly.
However, note that not everything you put after dialogue that contains a pronoun or a character's name is actually a dialogue tag; it is only a dialogue tag if it has a speech verb that directly describes the quote being uttered. So if a character says a sentence and then grins, then "He grinned" is not a dialogue tag; it's a separate sentence and should be punctuated as a separate sentence unrelated to the dialogue, like so:
She laughed. "That's stupid."
"
You're stupid." He scowled at her.
"Childish, are we?" She grinned. "You're amusing."
Note that if you have a dialogue tag that
also includes an unrelated action, that's punctuated like a dialogue tag because it still has a speech verb and so is still a description of the dialogue being said:
"I'm not sure," he said, twiddling his thumbs. "Isn't that kind of dangerous?"
"I guess," she said; her face fell.
"Well, we'll figure it out," he said, grinning in a way he hoped was somewhat encouraging.
And that just about covers it, except for some rare situations I won't go into. Try Googling for a grammar guide if something comes up that isn't mentioned here.
“I know... of your goal.......................... I know... I cannot beat you.”
An ellipsis is exactly three periods. Putting in more of them to lengthen the pause is something done in video games, but not in prose. If you want to show this as an especially long pause, write some narration in between that indicates this: "I know... of your goal..." The creature waited, taking a slow, leveled breath. "I know... I cannot beat you."
The creature shot opened his eyes
Either he just
opened his eyes, or he
shot them
open. "Shot opened" doesn't make any sense.
Although in the rest of the prologue you refer to the creature as "it", and in your preamble you explained all legendaries are genderless in this fic, so I'm presuming this "he" was a mistake. Be careful with this sort of thing; I also find it hard to stick to calling characters "it" (and in my fic legendaries, although technically genderless, are referred to with gendered pronouns anyway), but if you're going to do it, be very careful with your proofreading so that you don't accidentally mess up somewhere.
Three pokemon looked up at the boy expectantly in the forest clearing. The one to his left resembled some sort of tiny dinosaur, light green skin with very rounded limbs. Around the base of the neck-less head were small green beads, that went all the way around. Upon its head a large leaf on a stalk stuck out, just above the large red eyes. Below its featureless body were four featureless legs, each ending with a small white claw. A small tail protruded from its hind. This was a Chikorita, the leaf pokemon. It stood calmly, its leaf waving gently in the cool breeze.
Beside it was a small bird that resembled an orange chicken. Its bulbous head which rested on its small round body contained few features, most predominately a small cream beak, two blue shining eyes, and three yellow tipped feathers sticking up on top. Below its head, small wing-like limbs protruded from the top of its body. Below two cream sticks connected to scrawny chicken feet stuck out. It carried most of its weight on only one, the other slightly bent backward, in the air. This was Torchic, the chick pokemon.
To the right of the boy stood a blue dog-like pokemon. Instead of a tail, however, there was a large pale blue fin that stood vertical against its backside. Its body was light marine blue, but a pale blue underbelly beneath. It had four short legs, each with three undefined toes at the end. Upon its large head stood another vertical fin, the same colour as the blue had. On each of its cheeks were a strange orange star shaped gill. The boy was surprised when he didn't see any eyes, but they were prised shut. The creature was also quietly murmuring to itself -
You really don't need to describe what Pokémon look like in this kind of detail. It's a pretty safe bet that if someone is reading Pokémon fanfiction, they already know what Pokémon look like - and if they don't, the only hope they'll ever actually have an accurate image of the Pokémon in their head is if they look up the name somewhere and find a picture, anyway. Describing Pokémon is better reserved for when there is something interesting or unusual about this particular Pokémon that's worth commenting on; the POV character wouldn't be mentally picking apart the details of what their starter choices look like if they're already familiar with Pokémon. More in-depth advice on this subject can be found
here, courtesy of Negrek.
Behind him the girl yawned loudly.
Suddenly bringing up "the girl" as if we should already know there's a girl there is a bit jarring. If you don't want to mention her name yet for some reason, "the girl behind him" would work better.
Edward grinned. She knew that Nuria was only kidding
Presumably that should be a "he".
She checked her watch, and raised her eyebrows.
Common mistake, but there shouldn't be a comma there because "raised her eyebrows" could not be a separate sentence of its own; "and" only has a comma before it if there are complete sentences on
both sides (well, that and if you have a list of three items or more and use the Oxford comma).
Here, on the other hand, there should be a comma after "you", because the "Nuria" is a direct address, and there are always commas surrounding direct addresses.
In a story you'd generally want to write "okay", because "OK" is shorthand that doesn't really belong in prose.
Edward caste his eyes over to the Mudkip.
Cast. Caste is a different word.
“I'd like the Mudkip, please,” he said, loudly so the Mudkip could overhear.
"Overhear" is a bit of a weird choice of wording here, since overhearing something generally refers to hearing something you aren't supposed to hear; talking loudly so that someone can overhear you seems like an oxymoron. Just use "hear".
It's spelled "dodge".
You forgot the space between "face" and "lit".
Edward took the ball and held it toward Mudkip, the blue dog-fish turned into a red plasma and withdrew into the ball.
This is a comma splice, or a sentence where two full sentences are separated with only a comma. Commas aren't strong enough to separate two sentences that could stand on their own, as here; you need to replace it with a semicolon or add a conjunction such as "and" after it.
Also, "plasma" is uncountable, like "water"; you wouldn't say something turned into
a water, so you wouldn't say it turned into
a plasma, either. Just "turned into red plasma" would suffice.
In the second chapter, you write "your" instead of "you're" a couple of times. When it's short for "you are", it's written "you're"; "your" means something that belongs to you.
And now all it was was a blood soaked, crippled, pitiful creature
That would be "blood-soaked", with a hyphen.
That should be "Well, hello, Chikorita", first because "Well" at the beginning of a sentence always has a comma after it, and then because it's directly addressing Chikorita.
As soon as the Mudkip materialized, it jumped again to Edward's feet and whispering,
“Thank you, thank you...”
You've done this several times, but it's wrong. You've probably heard people say you should start a new paragraph with a new line of dialogue, but you only need to start a new paragraph when
a new character starts speaking, because paragraphs are meant to separate topics. There is no change of topic between a character doing something and the
same character saying something, so you don't need to put a paragraph break there.
How cheesey that sounded.
Cheesy.
He then reached into his pocket and brought out his bright pink Pokedex. After a second of silent internal fuming, he flipped it open and pointed it a Mudkip.
Earlier you said he didn't mind the Pokédex's color, just the nickname. So which one is it? Also, that should be "pointed it
at Mudkip".
Mudkip looked dishearten.
Disheartened.
Littleroot Town is only two words.
They soon came across another small clearing, and within were two dog-like creatures, with spiky, thick, brown and white zigzagging fur that stuck up on end. They had small, spiky brown and cream tails, and on each of their eyes were what resembled a black mask . Zigzagoon. A good start, thought Edward. They appeared to be sleeping under a tree on the outskirts of the clearing.
Another problem with such lengthy Pokémon descriptions: by doing it that way, you bring attention to things the character
wouldn't be noticing before things that he
would. Edward should note them as being asleep immediately, not only after mentally describing what they look like - otherwise the reader starts imagining them there playing or standing around until you suddenly mention they were asleep all along, and the effect is jarring.
and this time when it wince
Winced.
Pokemon heal far quicker than humans, that's why they can fight so long and hard, and don't mind doing so.
A comma splice again. That first comma should be replaced with a colon or semicolon.
Something clicked, the raccoon was thrown sideways.
Another comma splice, but I'm also just confused. Something clicked? What do you mean by that?
the breathe knocked out of him
Breath. Breath is the noun; breathe is the verb.
“Raa-AAA-aaalts!” it Growled at the grass type.
You generally haven't been capitalizing moves; don't suddenly capitalize this one, especially since this is a context where you generally wouldn't capitalize it anyway (since you're using "growl" as a speech verb here).
“Look at it, this Pokemon came to experience joy and happiness, but we bloody and bruise it and try to take away its free will. If it wants to be caught, that's fine, but we should ask it before we catch it. It should know what it's getting into.”
Well, that seems a bit hypocritical considering Chikorita seemed pretty enthusiastic about Tackling it. Just saying "Oi, don't go capturing it without asking" is okay, but with the fact she's also disdainfully mentioning the bloodying and bruising, you're just making her come off as unreasonable.
and through it at the wild Pokemon
The past tense of "throw" is spelled "threw". "Through" means going through something.