This was a rather short prologue, so I'm not sure why you put it in spoiler tags. Being a bit picky, but still. The formatting is odd. You want to hit the enter button twice when typing this out on forums, like how I'm typing this review out.
A
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Anyway, time to kick off this review with nitpicks:
Cyrus was getting close. He was on the back of his fastest pokemon; Rapidash.
The pronoun 'he' is used to refer to 'Cyrus' because it is the closest noun to it, and so it gets confusing, since I can assume the 'he' was to refer to Flint. You should fix that up. Also, the semi-colon before Rapidash is grammatically incorrect. You want to use a colon (:). Semi-colons are only used for separating two independent clauses. You mistake this a few times, so you want to back through your story and fix them.
Flint nodded, and Rapidash trusted Flint with it's life.
'It's' is the conjugation for 'it is.' 'Its' is the possessive form, which is what you want to use. You want to fix this up since you confuse this quite a few times in your story.
Below him he saw an huge red beam; Dialga's Roar of Time.
Huge doesn't start with a vowel, so you'd use 'a' instead of 'an.' Semi-colon is also inappropriately used here, just as before. You mistake this again in your story somewhere.
He could see that he was in pain.
Wait, what? You used it to refer to Dialga, so it's safe to assume 'he' is for Flint, but this sentence doesn't make sense that way. Clarification is needed here.
But he heard the Roar of Time zip past him. Over his head.
Is there a particular reason why the bolded bit is in a separate sentence? It's a fragment by itself, so putting it at the end of the preceding sentence would make more sense. And it readers better.
He would prefer to die by falling than to die by the hands of Team Galactic.
This is messed up logic, because technically Team Galactic did kill him if they shot down Drifblim. They kill him either way.
Okay, nitpicks aside, I suggest that you proofread your story for any sorts of technical errors. They mean a lot if you continually make the same mistakes, and you can surely fix them.
Flint having a Drifblim makes zero sense, and I don't care what world he's in. If he's not even Flint, then you might as well make an original character. Flint is a Fire-type trainer, and it's worked out pretty well for him throughout his life. You can't slap on Pokemon for Flint just because you want to. He has to have a reason, or it makes no sense. And in this case, it makes no sense, so I'm confused as to why you gave him a Drifblim. It didn't even do anything this chapter. Character wise, I'd say Flint was extremely out of character. He abandoned the Elite Four? That's unrealistic in two ways: 1) He just left the safety of that place. There are plenty of other Elite Four members as well as the Champion Cynthia, so it would be terrific to fight alongside them rather than running away. One isn't as as strong as many. And, 2) Flint is strong in his own right. He's an Elite Four member. He can battle Pokemon and knows how to deal with them, even legendary Pokemon. In the games, a ten-year old catches Dialga. Flint is well over that age. Why doesn't he even try to battle Dialga? He has a lot more Pokemon than Dialga could handle, since he has six while Dialga is singular. He might even end up defeating it. And besides, it's not in his character to run away.
So that's all I can say for a short bit. There are a few issues, and they are specific. You can fix them easily, so I hope you continue writing. I'll be sure to find out what's next.
