Hello, this is my first review, so I apologize in advance for my ineptitude.
Pikachu manifested in front of Ash, ready for his next task.
I find it odd that Ash kept his pikachu inside of a pokeball, for pikachu as far as I can remember avoids being trapped in a pokeball. I suppose that some sort of radiation could be present in the atmosphere, and pikachu's small body can't be exposed to it for a prolonged period. In spite of that, I think that pikachu would still insist on remaining outside of the ball, given that he did not return to his pokeball in this one episode where they were stuck in a mountain.
They would all start their own town again, host their own gym, find a way to rebuild this wasteland to the glory it once knew.
It is strange that they want to host a gym despite some sort of apocalypse that ravaged the world. It just seems as if Ash's priorities are faulted.
Nothing would stop him. The title of Pokémon Champion wasn’t there anymore as an end goal – this time, it was the safety of his friends.
I understand what you are saying, but this sentence is rather confusing. Perhaps a better way to phrase it would be, " The title of Pokémon Champion wasn't his goal anymore this time, it was the safety of his friends"
I have two things to mention about the previous excerpt. First, you use an em dash quite often even when a comma may be more appropriate. Second, you used the phrase "end goal" which is redundant as a goal is something that is achieved at the end; it is what you strive for.
This was only the beginning – nobody knew what lay ahead in this shell of what used to be a vibrant Pokémon world.
Again, I would switch the em dash with a comma. Also, when you say "in this shell of what used to be a vibrant Pokémon world" I feel that the statement is redundant, given that shell implies "what used to be", so in total: "This was only the beginning, nobody knew what lay ahead in this shell of a vibrant Pokémon world."
It was at once pleasant, but overwhelming: a reassuring sign that nature was returning to normal, but without notable season changes, traveling became that much more difficult.
A lack of notable season changes means that a large meteorite must have collided with the earth to tilt its rotation axis. That's some serious catastrophic stuff. In fact, I'd venture to say that Deoxys might play a significant role in the story given his extra-terrestrial origins.
It appeared to be a city that was rediscovered and turned into a fort, possibly for marauders or friendlies – Ash wasn’t going to take a chance and find that out for himself.
The em dash again.
“Prepare for trouble.”
“And make it double.”
“To scavenge the world after devastation.”
“To ensure survival within this nation.”
“To denounce the goods of compassion and grace.”
“To extend our reach to the wasteland’s face.”
“Jessie!”
“James!”
“Team Rocket! Blast off at the speed of light.”
“Surrender now or prepare to fight.”
“That’s right!”
You need to fix your spacing as it is not consistent with the rest of your story.
Jessie, James and Meowth jumped on their Growlithe and vanished into the dust.
I doubt that a growlite is capable of supporting the weight of two adults and meowth. Perhaps you meant to say
Arcanine?
“I can’t believe... I thought you were...,” Misty said, tears embedded in the corner of her eyes.
I don't think embedded is the appropriate term here as it implies being fixed in place, and we both know that tears are capable of moving. Just a nitpick, nothing major.
“We’ve been living in this wasteland for too long. We need to find a way to restore everything. We can channel the power of our Pokémon and those we encounter... let’s bring life back to this world.”
Cue passionate sex scene.
Overall, I have to say that you did a good job for your first fanfiction. In your next chapter you should avoid using em dashes so frequently. I can't comment much about the plot or character development as there is not much for me to work off of.