Over several millennium, Equestria had lived in harmony with the royal sisters in its lead. With the help of the ponies living throughout the land, prosperity had been kept, but now nature has begun to slowly unravel, weather has begun to act up in unprecedented ways, causing chaos that could put kingdoms around the world at risk. A secret is discovered, that Equestria has been waiting ever since the sisters walked the world, for one who will set things right once more, but at what cost? His life was mediocre in many ways, but there was always a dark power over shadowing him, turning his joys into sorrows. Finally, when he had found one last thing that made him happy, would he have to give it up?
This will be a three act story. I am doing my best to work on the story consistently, and please, this is my first FanFic ever here, so if you see this, I'd really appreciate comments, ratings, and especially critiques.
First! (just kidding
)
Your story is pretty good. The next things are more like nitpicks, small things who bothered me while reading.
Things I noticed: your grammar is good. I even saw some words that I had to look in a dictionary for what they mean. But I think there are too many comas. English is not my first language, mind you, but I feel like there are too many 'pauses' during the text. Also is it intentional that the names are written, like 'PinkiePie'? You know, without space? No problem with it, just curious.
=/
About the characters: I couldn't see much of their appearances. I didn't see how SparkWave look like and everything I gathered from FireLight is from the moment Spark is noticing the differences in his son, after the thunderbolt. I know they are secondary characters but still, I think it would be good seeing more about how they look like.
About Spark Wave choice: While I agree that such a pegasus would be dangerous to society, I keep thinking that instead of just exiling him he could go have gone into exile... with him. Besides, isn't it more dangerous to let his son being taken by a family who doesn't know anything about his power? He could have another surge and roast them. Still... when in time of confusion, it's kind of easy to take a bad decision. Was it because he was still shocked by his wife fate that he took such a harsh decision?
I will later read the other chapters. Don't worry through, your story is good: like I said before, those are more like 'nitpicks' I found while reading.
1010381 Wow, I really appreciate the comment!
In fact ever since I posted this story and began showing it to friends, I believe this is the first real critique I've received, in my opinion. So, first of all thanks for the complements, I have worked for quite some time with grammar and my vocabulary (Thesaurus are also great resources for creative writing). As for the commas, I do agree that I overdo it with them at times. I recently went through an English course at my highschool which had a large segment focusing on commas, so I try hard to be careful about how I use them and I always try to double check each placement. My biggest issue is that when I use commas, I've made a bad habit of writing the story how I would speak it out loud, which usually involves me using a lot of dramatic pauses.
As for names, yes, that was intentional. I may change the way I format their names later and remove the mid name capital. I also sort of left their appearances to debate on purpose when I wrote the first chapter, but I do plan on revising this chapter and changing the story around a little bit sometime in the future. I don't want to reveal anything, but there will turn out to be another reason for his choice, which is a bit more reasonable, and it will link to the end of the story (which is probably a long ways away).
One more thing, just keep in mind that this story of mine is, amongst other things, a bit of an experiment to test myself as far as story, characters, and plot, as well as to stretch the creative portion of my mind.
Chapter 2 done.
Okay, first the grammar: besides the commas, I noticed a few moments you used a word... but I think you meant another one.
For example, when you write "weather", didn't you mean "either"? That was at the scene the protagonist is talking with the squirrel. Also, at the phrase: “You can come on now, I’m not working no more, she’s gone out today.”, wouldn't it be better "out" in place of "on"... and "anymore" in place of "no more"?
About the history: I have to say that Thunder and his squirrel moments were Daww worthy.
Also mother and son moments always move my strings. :
Another thing that caught my attention is the author notes: you said that many tragedies start happy. Does this mean things will get pretty bad from now on?
Keep safe.
1017240 Hey, again, as I said in response to your last comment, what I said about my comma usage remains the same. As for words, thanks for point out "weather" I'll fix that shortly when I have a moment. With the character Thunder, though, I made messed up the grammar there intentionally, because he is a very young pony at this stage, and is bound to mess up his speech.
In response to the query about how sad the plot will be, yea it will start to get a bit tragic, but not for another few chapters. I just posted that on this chapter because of how happy and uppity it was. Oh, and another thing to keep in mind when you continue reading this, is that the main area of this story will take place in Thunder's adulthood, so the first several chapters have large gaps of time between them.
Chapter done.
Things I noticed: there were some instances you didn't use the big 'T' in thunder. Fluttershy reaction truly made me giggle.
Also, is Thunder faster than Rainbow Dash?
1022765 Well usually when I don't use a capital 'T' in thunder, it's because I mean actual thunder, not the character Thunder, but I suppose I'll check to make sure I didn't miss any capitals by mistake.
As for how fast he is, you'll just have to read a bit more to find that out.
Chapter read!
Well... strangely, I don't have anything to add at this point.
I will read the next one later!
Woah, it was been more than a month. Sorry about that.
Well, back on my reading schedule. Chapter read!
I got the story very well. The only thing I wonder is how the guards already had a royal proclamation of the princess? Perhaps when the first incident at that race happened she warned her soldiers to keep her eye on him?
Back to the chapter, now that is what a call a circle of misfortune. I think that Diabolous Machina had a lot of fun with this chapter, lol. XD
Also, shouldn't Rarity be a bit more compassive? Well, until the next chapter.
Chapter read.
First thing I noticed: I liked how you did your best to avoid a time paradox. Really, those things are serious!
However... I kinda got creeped at the eye scream part. You know, when I read something I try to imagine every scene... that was kinda disturbing.
1260737
Well thanks a ton for the new comments
and yea, i'm going to be doing my best to avoid canon manipulation with the other 2 acts as well. You might be right about Rarity, but if you look closely at all the background events going on, she was still a foal when she appeared in that chapter, so i figured at that young age, coupled with her current personality, i thought it'd be better to go with a more "I'm staying out of it" sort of attitude. If the eye scream part creeped you out, then hopefully that means i'm doing a good job with detail. 
And finally, keep in mind the story is still young and i've thought very far ahead, you'll eventually find that there is a reason for which the guards had arrived so quickly, and even if I didn't, it's based off a cartoon, stuff like that happens all the time. 
But nah, i'm sure Celestia had a good reason for this.
Also, I'd just like to say that I'm really grateful for the wonderfully productive comments, I wish I could get more people to comment, but still, stuff like this is what makes me want to keep writing
and I do hope you check out the next story I write (Which I may start before I begin writing Act 2 of this story). I thought I might try my han-er I mean hooves, 
at a Sparity romance fic. I'm not real experienced in writing romance, but I do have good ideas of what romance is at least.
Chapter read!
Wait... when did Fluttershy meet Thunder? I mean, like really met? Perhaps I am not getting very well the time transition here.
Besides, why didn't she take him to the hospital?
Those were the two questions that kept through my mind.
Chapter read!
My biggest question for this chapter is: why didn't Fluttershy and Twilight tell her friends? It's seem kind of weird the elements of friendship didn't share their find... even through there was strange all over it.
And now for the overall story:
The things I liked: The story was concise. I could get a good grasp of the history and there were many moments who were heartbreaking. I could add a lot of other things, but I already told them in my other comments.
The things I disliked: First thing, I have nothing against characters who have special powers. In fact, I think it's interesting to give them different kinds. Still... your character seem kind to be in a different tier than somebody else. It seems you are going to put a villain, an evil side or something like that later... when you do, try to don't make it seem like only your character could defeat it.
Second, the diabolous ex machina kind of got carried away. It was bad stuff after bad stuff happening. I want to add I have nothing against very tragic stories. I can appreciate some tragedy. It all just seemed so... connected. Everything resonated to try to make the main character was miserable as possibly.
Third, a lot of people get touchy by OC x Canon relations. I don't know if you plan to make this shipping or just friendshipping... still I think you should go a bit slower with it. There were several moments (like when Rarity or Twilight) seemed to leave, just to keep Fluttershy and Thunder together. Different from many, I have nothing against it. But I think you should take it a bit slower.
And now, a personal suggestion: Perhaps you could add a sidestory? You know, focus on another character... like Rainbow Dash? That would remove the spotlight from a single character and give you the chance to expand on others.
I will fave this story and I will repply to your other comment in an instant. Don't worry about it, it was pretty good. Also remember that what I liked or disliked also differs from other people tates.
1261521
A Sparity romance would be a shining idea!
If people read your canon character history and enjoy your writing style, I am sure you would get many commenters in this story as well. 
Because sadly most people avoid OC stories, believing that most of them are self inserts.
Sparity is also very popular, that could net you many views!
---
Ah, now I noticed you named your history Act - 1. May I give you a suggestion? It's usually not a good idea to write 'it will be continued' or 'the first story'. Because if you decide to focus on other histories or lose interest it kind of binds you into continuing it.
1265271 OK so, again thanks for the great comments, I really appreciate them
First off, about the hospital thing and Flutershy/Twilight not telling the others, this is somewhat vaguely suggested why by the story, but in the future i planned to make it a bit more thoroughly understood. Also no, I wont create a villain that only Thunder could defeat (Hint: The villain is canon). You will also discover why Thunder ran into so many tragic events so quickly. Yes, the story does revolve a bit around Thunder and Fluttershy, but if the reltion does end up moving beyond friendship (not saying whether is will or not) it wont happen until very close to the end of the story, because I didn't intend this to turn into a romance. I have had thoughts about little side stories within it as well, though they may be more about Thunder's relations with other characters, not just those characters themselves.
Thanks for supporting my plans for a Sparity story as well
i'm still not certain where i'll go with it but when I do get around to it, i'll be sure to try my best. 
I wasn't expecting a huge response from this story either, I knew the OC stories weren't super popular, and also, by labeling the story Act-1, yes I did point out there will be more, but I didn't really specify how much more there will be, so I left myself with some freedom.
1288573
No problem. And you're welcome!