To be truthful, it wasn't that original, but then again it is just for a Magikarp. It works, however, probably the reason why the plot in question is used a lot. For your future stories, however, I might suggest introducing slightly more of a plot.
Also, the story was mainly speech- this isn't really a good thing to have. I also got a feeling that it was a bit rushed, and putting in more story and detail could help with that.
No offense, but this area could use quite a bit of work. One of the recurring things I saw in your story was the use of apostrophes with plural words- it's actually unnecessary. For example, in this section-
So when they got to aqua city it was full of trainer's with water types.
-the apostrophe in the word isn't needed. That implies that the word is short for 'trainer is', which makes no sense in the section in question.
Also, when someone is speaking, please place the speech in quotation marks or differentiate the text somehow. Without one of these options, it makes it quite difficult to read.
There were also a few cases of missing capital letters- they have to be placed at the beginning of each sentence as well as each speaking portion.
I also noticed that in some sentences there was some missing punctuation, for example-
"awww man fine then Pichu Quick attack follow up with Thundershock"
This sentence just looks like a huge run-on, to be honest. There needs to be some more punctuation; if you were to read it aloud without stopping, then it would seem rather rushed. I would probably change it to something along the lines of-
"Awww, man! Fine then- Pichu, Quick Attack, then follow up with Thundershock!"
In some places, there was incorrect spacing- one space should be used after punctuation, and no spaces before it.
Overall, running the story through a spell checker/grammar checker should help get rid of some of the more basic errors, but reading over the story a few times can always help; spell checkers can be wrong.
Sorry, but there was next to nothing there. I had no idea what Aqua City looked like, nor the Gym, the Gym Leader, the trainers or where the battle happened. It also would have helped if you described the Pokemon- most of the people on this site know what a Pichu looks like, but if someone doesn't then they'd be utterly lost.
Also, describing attacks helps spice up a battle. If you just said that Pichu used Thunder, then we don't know if it hit or who it hit, which could seriously make it hard to keep up with the story. I advise you to improve on this section in the next story you write.
When it comes down to it, Pichu only used two attacks, one of which doesn't deal damage. We both know that a Pichu could easily wipe out the Karp, but it doesn't have to be that realistic and linear! The Magikarp in question could be assisted by a Gyarados, or about ten more Magikarp. Also, I can't really see how Pichu was made deaf by a Flail, and how deafness was healed by a Full Heal. I'd try improving on this section too.
About 900 characters short of the minimum.
Magikarp not captured!
Sorry, but there wasn't really enough here. Don't give up, though- you have a very good story here, but it needs a little improvement. Notify me when you've edited the story, and I'll be happy to give you a regrade.