Alright, I suppose I'd better start with the plot sypnosis since that will actually answer most of the questions that I've been asked with a little Q&A after for those questions that aren't answered by it.
Pinkie wanted to keep hiding from her feelings and was given the chance to do exactly that but just going straight back into trying to make ponies laugh off their troubles made Pinkie come to a different kind of realization and she decided to bide her time.
Applejack was given the information that she wanted about a way to possibly save Apple Bloom's life and went to Sunny Town but figured out that what she found in Sunny Town wasn't what she wanted. What she really wanted was time to work through her grief and come to terms with what had happened and so the entity stole the Super Speedy Cider Squeezy 6000 and left it at Sweet Apple Acres and Applejack fell into the trap and would have became rather slothful. This corruption of Applejack's spirit and Element caused her Cutie Mark to begin to blacken until it would have become entirely black and only outside influence would have shaken her out of her slump.
Fluttershy wanted a chance to help out, but considering the situation wasn't really in the right situation to do so. To 'fix' that, Nightmare Diamond provided Fluttershy/Cruel with the perfect patient, one that would never get better and would need their help for as long as 'Shy would give it. 'Cruel almost messed it up by provoking an incident similar to the one from the Re-harmonized series that caused 'Shy to turn into Nightmare Whisper, but the entity's efforts to 'peacefully' remove the Mane Six as obstacles caused some unexpected, but appreciated, feedback between the Re-harmonized world and the main series that headed off the incident. In the ensuing argument, 'Shy made the rash statement that she wanted some peace and quiet and the entity used the off-hand remark as a way to pull 'Cruel from 'Shy's head and set her adrift between worlds. Fluttershy's corruption sunk in and she would have become obsessed with tending to her one patient.
Rainbow Dash was going to find herself being given an offer to join the Wonderbolts with the sponsorship of one of Canterlot's elite (Fancy Pants) and would have been forced to confront one of the intrinsic problems with Loyalty that being conflicting loyalties. Rather than abandon her loyalty to her friends or her dream with the Wonderbolts, Dash was going to end up running herself ragged trying of meet the obligations to her new flight team and friends at the same time which would have left her with very little time to worry or fuss over anything else to the dismay of Scootaloo and Twilight who tries to talk to Rainbow about the problem that she had mentioned before. She would have worked herself to exhaustion and thus been safely out of the way, though this was vastly preferable to one of the bad ends were Dash ends up transforming into a Nightmare and joins forces with with the entity to accomplish their mutual goals.
Twilight was going to continue her research into a way to solve Trixie's condition and 'accidentally' come across a scroll that had information on a 'cure-all' spell that was very similar to her failsafe spell that would be able to fix up Trixie's condition in just a few moments. However her own research and advice from friends makes her realize that this magical solution isn't what was necessary and she goes into Trixie's mind in a manner very similar to the way she does in alexwarlorn's story. Once she's in there though and confronted with Loneliness and the very obvious danger that it presents, Twilight does her best to solve the problem the way it should be handled but gives into temptation and uses the 'cure-all' which does exactly as advertised and gets rid of Loneliness...by shunting it into someone else and inuring Loneliness to more mundane treatments. Realizing what she's done, Twilight does her best to track down where Loneliness has gone but finds the only thing working to be the Cure-All that just keeps shunting Loneliness away to others something that Twilight is...well...horrified by so she pursues it as best she can to end the swiftly growing threat that Loneliness represents.
Things have honestly gone downhill for the Mane Six at this point but it seems to be happening for every one that seems to be capable of standing in the entity's way. Celestia's desire to be normal and just interact normally with her subjects is given to her via her magic being stolen, which fulfilled what Luna wanted, being appreciated by the subjects since the duty of handling the sun and the moon falls on her as well as protecting Equestria from suddenly emboldened old enemies try to carve up Equestria. Those are just a few examples, but it should give you an idea of what would have been going on which is about the time the scene would have cut back to Pinkie being consoled and given advice from Happy about how laughter wasn't what was needed at the moment when Pinkie notices the troubles that have befallen her friends and moves to help them. Happy protests and tries to argue that, as a part of Pinkie, Happy knows what Pinkie really needs just for Pinkie to reveal that she's known Happy wasn't a part of her the entire time since she'd have never named a part of her personality 'Happy Pie' when there was an obvious pun in having her 'happy' side named 'Cheery Pie' which sounded like Cherry Pie, you know...the sort of thing Pinkie would have noticed nobody else probably would have. The revelation that Pinkie has known all along and her Cutie Mark hadn't blackened causes the puppet master to finally reveal herself. A creature calling herself Nightmare Diamond appears and chases Pinkie out of Ponville and into the Everfree. It was also the only time that I had planned to do a song, a ponified version of 'In the Dark of the Night' from Anastasia as Nightmare Diamond uses her magic to get those she's 'helped' to drive Pinkie towards a specific location.
In the dark of the night I was tossing and turning
And the nightmare I had was as bad as can be --
It scared me out of my bed --
A foal falling in red!
Then I opened my eyes
And the nightmare was...me!!
I was once the most fashionable mare in all the town.
When the royals betrayed me they made a mistake!
My curse made each of them pay
But one little mare got away!
Little Pinkie, beware,
In the dark of the night evil will find her
In the dark of the night just before dawn!
Revenge will be sweet
[DIAMOND AND CREATURES]
When the curse is complete!
In the dark of the night
She'll be gone!
Oh oh oh oooooohhhhhhhh!
I can feel that my powers are slowly growing!
Tie my sash and a dash of perfume for that smell!
As the pieces fall into place
I'll see her crawl into place!
Dasvidanya, Pinkie, you fool, farewell!
In the dark of the night despair will strike her!
Despair's the least I can do!
In the dark of the night evil will brew.
Soon she will feel that her nightmares are real.
In the dark of the night
She'll be through!
In the dark of the night
Evil will find her
In the dark of the night terror comes true.
My dear, here's a sign --
[ DIAMOND AND OTHER MANE FIVE SANS PINKIE]
It's the end of the line!
In the dark of the night...
In the dark of the night...
In the dark of the night...
Come my minions,
Rise for your master,
Let your evil shine!
Find her now,
Yes, fly ever faster
In the dark of the night...
In the dark of the night...
In the dark of the night...
She'll be mine!
The specific location being the Mirror Pool where Nightmare Diamond tells Pinkie that she has the choice of saying the rhyme and summoning a duplicate or having everything she's given their friends taken away and once Pinki has, Nightmare Diamond banishes Pinkie into the pool and releases her control of the remaining Mane Six to return them to their Gilded Prisons.
Cue a not insignificant time skip into a pseudo-bad future where Pinkie is freed from the Mirror Pool by a few old friends, probably Trixie, the remaining Crusaders, and Spike for Pinkie to discover that Equestria has turned into a nightmare land. Nightmare Diamond is waging a war against Equestria and seemingly everyone who hasn't fallen under her sway in an effort to take Canterlot for reasons that no one really seems able to figure out while her best soldiers are 'rewarded' with a Gilded Cage were they get exactly what they want. Pinkie immediately decides to set about freeing her friends from their Gilded Cages so they can set about finding out someway to stop the Nightmare before she can get to Canterlot.
This is accomplished in relatively short order except for the fact that no one has seen Rarity since Nightmare Diamond began her campaign and Twilight (who would have been rescued last) reveals some information she was able to figure out while chasing down Loneliness (her Gilded Cage). The only thing connecting all the people who were trapped by Nightmare Diamond before the war started was the fact that they were all part of the same social circle and that the only one able to arrange some of the things that had happened would have been Rarity. The theory is, understandably, unwelcome but it is proven when they attempt to use the Elements of Harmony (Spike as a temporary stand in for Generosity) against Nightmare Diamond just for nothing to happen. Nightmare Diamond is Rarity and her own more powerful connection to the Element of Generosity, albeit one that has become twisted and blackened by her actions, protects her from the Elements. They demand to know how this has happened and how Rarity could have done this to them and Rarity is more then willing to explain.
Back at the beginning of the story was right in the middle of the re-harmonizations after the Day of Chaos and it took place after Rarity's -, but the thing was that the biggest difference between Rough Diamonds-verse and it's Heart World is that when Rarity threw the circlet that cut Sweetie Belle's cheek, Rarity didn't 'miss' and accidentally killed her sister in the middle of her breakdown. Because of such emotional trauma at such a critical moment in her own re-harmonization...well...Rarity came to the realization that people didn't know what they needed and all they desired was what they wanted and what they wanted could hurt them as much as it could be good for them. So she decided to give every pony what they wanted as a final gift from her to the world before finally taking the chance to give herself what she, a way to make it as if Sweetie Belle had never died. The Gilded Cages she had used on her friends had been her attempt to keep her friends from stopping her without actually hurting them and she had just moved on to inflicting them on others once she saw how effective they were. Seeing how they didn't work though, Nightmare Diamond prepared to use more lethal methods and the Mane Five beat a quick retreat to try and figure out how to fix the situation.
While they do that, Nightmare Diamond does the unthinkable and strikes a bargain with Entropy for the Elder's aid in taking Canterlot in return for an unknown price. With Entropy's aid, gained through absorbing an avatar of Entropy much like Discord had eaten Havoc's during the war, Nightmare Diamond is able to take Canterlot and prepares to finish it all. Her plan has been to take Discord's statue, practically an anti-thesis to most positive things, and infuse it with Entropy's power before dumping his body into the Truth. She figures that the reaction between the Truth and Discord will fracture the world, and perhaps the Truth, enough that she will be able to rewrite the history of her world to give everyone what they want but, to do so, will inevitably pull the Rough Diamonds-verse between the Re-Harmonized Heart World and the show's Heart World. The rewrites to the world would have clashed so heavily with 'canons' of both worlds so heavily that Rough Diamonds-verse would have been annihilated in the resulting backlash from the two Heart Worlds even if it was briefly preceded by a 'perfect time'. This is actually the reason why Apple Jack has been having headaches this entire time and why nothing happened in her dream, their world has already begun to realign in the past , present, and future with what Nightmare Diamond wanted and thus the changes were both the Truth and Not-Truth, even by the standards of the multi-verse visible through the Truth. Nightmare Diamond had already succeeded in infusing the Truth with Discord's tainted essence and had begun to rewrite the world to how she wanted it to be although she quickly discovers that some things cannot be changed, things like the dead returning to life within their own world. The realization that she had never actually been able to restore Sweetie Belle to life and now probably would never see her in the afterlife has a devastating effect on Nightmare Diamond.
While that is happening though and while the 'perfect period' begins, the Mane Five and friends desperately try to figure out a way to stop Nightmare Diamond and save Rarity at the same time. They end up following through on several false leads but in the end none of them really pan out and they come to terms with what must be done to save their world. The Mane Five and friends move to assault Canterlot and Diamond's/Entropy's combined forces so that they can retrieve Discord's statue and stop the chain reaction that would begin tearing their world apart. I would go into more detail here about things like the battles going on, who sided with whom, what happened to Diamond Tiara, and so on and so forth but I think this journal entry is beginning to drag on a bit. Plus those things only serve to push the plot forward, not actually move it along so not that worried if I don't go in depth on how they went down. In the end they finally begin to battle with Nightmare Diamond herself, holding nothing back in their attempts to put a stop to her scheme. Eventually though, they are triumphant in 'rescuing' Discord
from the Truth and Diamond's grip on reality falters and things begin to return to how they should be.
Nightmare Diamond still exists though and it's obvious that she'll just continue her attempts to bring Sweetie Belle back or, even worse, move to another world and replace herself there bringing her curse to others so they have to figure out some kind of more permanent solution to a Nightmare that cannot, no, will not be redeemed. At which point I would have had another 'vote' on the matter where the readers would decide Nightmare Diamond's fate and I would go on to write the epilogue from there.
That....uh...is the rough synopsis and it was pretty much entirely derived from an off-hand comment in one of alexwarlorn's non-main story chapters where Celestia and Luna are making abstract references to the many different pony-verses and their relation to the main heart world (the show) and how becoming too different from it could result in backlash that destroyed that world (fic/video/game/etc.) from angry Shadows that Watch (fans). I decided that made for one helluva scheme for a villain to attempt, knowingly or not, and the evidence of that is the ten chapters and hundred some odd pages that you've read.
Now a lot of the questions asked were answered above, but here's some that could be answered more specifically.
What was the significance of the butterfly, that Fluttershy took care of? Was it really a butterfly?
The significance of the butterfly was that it was a creation by Nighmare Diamond to lure Fluttershy into her Gilded Cage and it was more a magical construct than anything else. Why a butterfly? Because it's her Cutie Mark and Rarity knows Fluttershy likes them.
What was the fate of Rover's dad?
He was briefly kept in a mental health institution in Canterlot before he was given back to his people where he was tried for attempting to incite war and thus a war criminal. Due his, apparent, madness though, he served a closely monitored prison term under the scrutiny of of his people. He never really recovered from his mental break, but he never demonstrated any further violent tendencies.
Did Pinkie eventually get better?
Pinkie was never 'ill', she was just sad and then determined.
Would Discord have eventually played a part in the story?
Eventually, but not as a mover and shaker himself. His mother, Entropy plays a bigger role than Discord and he mostly exists as a tool that is used by the real main villain to enact her plan.
It would have been explained in the next chapter, but the young ponies weren't in any real danger as long as Rover was there. Once he lead them in there, he retrieved a sack of animal meat he kept stored inside of the crypt and gave that to Fifi and told the foals to keep screaming until he was sure the other dogs were gone. Once they were he lead them out and tunneled up the surface were he kept them hidden while he tried to figure out what to do with them, Apple Bloom and Diamond Tiara eventually convinced/cajoled him into doing the right thing though and Rover lead them back to Ponyville but bailed before the adult ponies saw him and figured out the truth. The bones in the crypt actually came from the animals Fifi had been fed before along with a few old pony bones Rover had tossed in there to mislead Rex along with personal items like Twist's glasses, Diamond's tiara, etc. The sham wouldn't stand against an in-depth investigation but that isn't something Rex could do or the Mane Six at that moment.
Where did "Happy" come from during Pinkie's chapter?
Happy was Nightmare Diamond in disguise but after the nightmare left, she used Pinkie's desire to be reassured that she was doing the right thing to create a mental construct that became Happy Pie.
What's up with the partially blackened cutie marks? For that matter, what motive does the butterfly/stormcloud/thing have?
A physical sign of mental corruption and control. Grief.
From a previous journal, you mentioned there being a "perfect order" of events. If I remember correctly, you were going to keep Rarity's chapter set as the sixth one regardless of how it went, so is there any chance you could tell us which choice would go towards this "perfet order," Rainbow Dash then Twilight, or Twilight then Rainbow Dash?
That comment I made was actually a bit misleading as the sixth chapter was less Rarity's and more the 'coming out' chapter for Nightmare Diamond. However the remaining order was Rainbow Dash then Twilight because Rainbow Dash needed the help of Fluttershy and Pinkie to get through her chapter but the longer she had to wait the worse off she was while Twilight needed advice and emotional support from the majority of her friends (as befitting the Element of Magic). Then Rarity's/Nightmare Diamond's chapter would have come.
What sort of entity did Rex make a deal with? And is Rex possesing Rover now? Or is it the work of the entity?
(I'm using entity for lack of a better term, just because I'm going by my memory. Which has failed me before...)
A nightmare made flesh but once Rex got captured he wasn't of any use to the nightmare anymore and was discarded.
Also, in another previous journal, you set up something of a scavenger hunt for artwork relating to "Rough Diamonds." Did anyone ever find it, and does it still exist? I know I couldn't find it. Then again, I've never really been good with scavenger hunts...
I do actually!
The first I comissioned is this one...
I even wrote the little blurb story that went along with it, but the formatting on it went flippin' crazy once it was put in a description box
and then there is this one...
which was the original design idea of Nightmare Diamond.
What happened to Sweetie Belle? Was it another group of Diamond Dogs that snatched her, or was it something else entirely? And why was Apple Bloom seeing visions of her in the caves?
Sweetie Belle, sadly, was the reason that Rarity became a nightmare in the first place. The minor difference that set off the chain of events in Rough Diamonds actually happens in Rarity's reharmonizing chapter when she throws the circlet at Sweetie and cuts her cheek. In the universe of Rough Diamonds, Rarity 'missed' the wall and ended up accidentally killing Sweetie Belle. Sweetie's spirit was trying to contact Apple Bloom, which is why she saw visions of her in the cave and would have continued to do so throughout the story to try and give advice and knowledge.
One of my favorite things in MLP:FiM and the Re-Harmonized stories is the sisterly relationship between Rarity and Sweetie Belle and I wanted to take my own crack at portraying such a pair of loving sisters.
Well, I think that's it for my questions. The only other thing I have left to say is thank you for sticking to your promise to not just drop this project, but to try to at least summarize tying up any loose ends.
No, thank everyone who did take the time out of their days to read my little pony fan fiction and were kind enough to leave comments and thoughts about how it was going. I never would have kept it going for as long as I did if I hadn't known that there were actually people interested in what I was writing about. I really, really don't like leaving questions unanswered in things I write/DM for so this was a big relief to get these details off of my chest. If these raise any other questions then just leave them in the comments and I'll get to them!