Firstly, there's no real need to put it in a spoiler, although I guess it's up to you. Just a bit odd with fics is all. And secondly, welcome to the forums!
The story was pretty decently written, especially considering that English isn't your first language. There's some small things here and there but overall it's understandable and also enjoyable to read. I quite liked the atmosphere of the first half of it, and the plot itself is also pretty interesting. I liked the narrator of the second half as well as he seemed more personally engaging than the man in the first part for myself - the latter seemed a bit more of a cardboard cutout so maybe consider showing some more character of the ambush Sharpedo guy. In short, it is a good beginning.
One thing I'd suggest to look out for is how you start sentences:
The ambush was just perfect… no contingency could crush that conviction.
The squad was the fastest one you could form in Hoenn. The Carvanha recruited for the mission belonged to professional swimmers. The Pelipper were caught at Evergrande City’s cliffs.
For instance in the beginning a lot of sentences in a row started with 'The' which does start to get a bit repetitive after a while. On that note however this wasn't a common problem.
A Castform would summon a heavy rain which could conceal them from enemy’s eyes.
'enemy eyes' is how the expression is often said, or alternatively you could go with 'the enemy's eyes' if you want to refer to a specific enemy, be it an individual or group.
They even had precious information about the rival captain: one out of the three Gyarados escorting his fleet, was able to perform electric attacks.
The comma after 'fleet' is unnecessary.
Seconds before the clash, a pale flash of light, followed by a deafening thunder, made them to bend down their heads.
Same here with the comma after 'thunder' (and arguably 'light' as well). I'll also add that 'made them to bend down their heads' sounds a bit clunky and wordy - keeping it to 'made them bend down their heads' says the same thing just fine ('to' is unnecessary).
Whit the Sharpedo’s aquajet they dodged the first one and knocked down the rider of the next one, in the same quick movement.
'Whit' means a very little bit - maybe you meant to type With. Also the move is known as Aqua Jet (two words) so I'd suggest typing it as aqua jet given you're going the uncapitalised route with attacks.
No sooner were they submerged again, a weird light surrounded the fainted pokémon and was followed by its transformation into a pink little mass, with no defined form.
The first part sounded a bit odd, partly because it feels a bit disjointed with the rest on either side of the first comma. It also just sounds weird so I'd suggest rewording the sentence, or at least the first part. (And heh - I had guessed the extra Gyarados might have been a Ditto).
Among all the words I heard from him, these, the most casual and free from wonder, would be the ones I would curse and bless so many times; the ones able to survive my consciousness’ indifference and, even after that, would keep echoing from my depths until being part of every action, latent, hidden like a Carvanha shoal beneath a dark wave… I’m sorry, future reader.
This one also sounded a bit weird in that it's a run on sentence and somewhat overwordy. Either cut down on the verbose description of the words' effect on him or split into two or even three sentences.
A neat beginning however! Good luck with the rest of your fic. =)