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I've been getting a long of comments, asking if there's gonna be a sequel, or if I'm gonna write an aftermath series of comics, and overall conveying that they'd like to see how this new version of Equestria has been changed by the events of this story. Now, I don't have the time, or inclination to write them with the level of fidelity you see here, but I do have an overall outline of the changes to the known seasons, and how this would fit into the show's episode listings.
1. The Night the Magic Died would take The Crystal Empire's position as the Season 3 opener. Picking up where the events of A Canterlot Wedding left off, it would serve as a solid fix for the season 2 finale's inadequacies, and kick off a engaging new dynamic that would play throughout the coming seasons.
2. The Crystal Empire would be moved to the middle of season 3, and the relationship between Celestia and Twilight would be changed to reflect the aftermath of the new opener. Twilight, rather than worrying over "passing the princess's test," her concerns would instead be coming to terms with being Celestia's figurative Knight, and no longer having her clear guidance as a teacher.
3. Magical Mystery Cure, Keep Calm and Flutter On (sorry, Discord fans) would be omitted from the timeline to make room for the new opener. In the original timeline, Celestia chose to release and rehabilitate Discord so that he might aid against Equestria's enemies, but after befriending Nahmat, such a risky thing would no longer be necessary, with Nahmat making a far more reliable "secret weapon" than he. Also she wouldn't be a pesky jerk like him. Being a jerk doesn't make you funny, edgy or cool. It just makes you a jerk.
4. Princess Twilight Sparkle, the opener of season 4, would be renamed as "Alicorn Twilight Sparkle," and would be mostly unchanged from its original script, except for the following:
4.1 It wouldn't merely take place on the summer sun festival, the episode would also start at the end of Twilight's official graduation ceremony. Afterwards, when Celestia and Luna are found missing, with night and day clashing in the sky, Twilight, as Equestria's first Celestial Magician in over a hundred years, would be appointed as leader during the crisis.
4.2 Nahmat would be called to aid once more, but due to being needed at such short notice, she would appear as an Astral Projection, summoned from the depths of Nahmat's mind while in deep meditation, and would only be able to assist with her observations and council, which would prove indispensable throughout the course of the case as she:
4.2.1 Urges Twilight to try her magic on Zecora's potion of revelations, despite not being an alicorn, reminding her that with Insight, she could recompose her magic to do so.
4.2.2 Deducts from the vision of Celestia and Luna's sealing of Discord, that he is the cause of the creepers crawling out of the forest.
4.2.3 Encourages Twilight to press onward along with her friends, even though they feel she should turn back for the sake of her safety and Equestria's need for a leader incase Celestia and Luna aren't found, stating that "Yes, Equestria needs a leader, but she needs her leader heading onward, to confront what threatens her."
4.2.4 And last but not least, when the team arrive at the Tree of Harmony and all realize that the creepers are an act of ransom against the world for Discord's release, she assures them that such a concern is moot, as she comes to the opposite conclusion. For the Tree of Harmony, once restored to power, would likely be able to hold the seal for far longer than the elements when left in the hooves of shorter-lived beings.
4.3 As Twilight gives up the elements, and the Tree of Harmony regains its power, the overwhelming energy surge transforms her into an Alicorn before everyone else's eyes, hence the tittle of the episode.
5. From then on, Nahmat's intermittently appearing phantom would fill the role Discord did, until Twilight's Kingdom, where she appears in person once again. I don't know how, precisely, it would change Three's a Crowd, but it would subtly change Twilight's Kingdom in the following ways:
5.1 Nahmat would be far more sympathetic to Twilight's existential crisis, although she would be dubious of the comforting advice from the other princesses that she will "play her part," instead remarking that "as being of volition, it is far more important that we live to make choices, rather than live to fulfill destiny." but "with that in mind, I'm certain you will get to make some important choice very soon."
5.2 Again, Twilight is reminded of the importance of choice when she reads a note from Nahmat, slipped in on the latest page of the diary while reading Nahmat's bookmarked entries, remarking that each of the other element bearers had to make a choice about what conflicting values they deemed best to be true to.
5.3 Tirek's medallion, rather than being a memento of his treacherous brother, Scorpan, serves its purpose as his secret weapon. When worn by anyone other than he, it burns away the wearer's will, replacing it with that of Tirek's, whenever they try to use magic or attempt to take it off, whether by themselves of by the aid of most others. He uses this to defeat Nahmat when they confront one another, since he can't take her magic as his own.
5.4 Though beaten, Nahmat escapes, and begins a journey to Tartarus, in search of the means to remove the medallion, but not before alerting the royal sisters of her failure. From then on, the episode plays out about the same, until the confrontation between Twilight and Tirek, where at this point, Nahmat returns and fights alongside Twilight, until…
5.5 …Tirek, not able to be beaten even by Twilight and Nahmat's combined strength, offers to trade the lives of her friends for the Twilight's magic. Nahmat points out that this is the choice she foresaw in Twilight's future, and urges her not to give Tirek what he wants, noting that unlike her friends' choices, the choice that would be in line with Twilight's element would not be for the greater good.
5.6 Twilight, her mind flashing through everything that lead up to this moment, realizes what she must do. She disregards Nahmat's advice, and gives up her magic for her friends' lives. When Nahmat questions her, she tells her that she knows who she is now.
5.7 "I am not Twilight Sparkle, the Princess of Magic, I am Twilight Sparkle, the Princess of Friendship. As princess, I, alongside my friends, have spread the magic of friendship across Equestria." Nahmat's mind flashes to all the decisive moments where each of her friends did exactly that. "That is the role I am meant to have in this world! The role I choose to have! You my not agree with it, but that is the choice I have made, just like you said I would."
5.8 Nahmat, realizing that cynical pragmatism, although easy, was not necessarily right, also realizes that she is Twilight's key-giver. She gives Twilight six strands of hair from her mane, to mach the six elements, proclaiming them to be Twilight's key, and thanks her for what she taught her.
5.9 The episode closes off, with the defeat of Tirek, the restoration of Equestria, and Nahmat musing on the tree's plan to disperse its seeds across its world, laughing at how, just as she planted the seed of her world's Power of Insight in Equestria, it has planted the seed of the little ponies' Magic of Friendship in her, and thus, her world.
Thus is the story of how Twilight Sparkle came to be the Princess of Friendship in the altered timeline. You're welcome to take it as you will.
More importantly, though, I disagree with your assertion that Discord was reformed in order to be a secret weapon. Rehabilitation is a worthwhile end in and of itself, and believing that Discord can be reformed is all the reason that's needed to try. The potential for him to be useful is an added bonus, but 'Tia didn't know when she tasked 'Shy to work on him that she'd later need a being who can sense magical disturbances.
Nahmat, if taking the place of Discord, would likely bother Cadance and Twilight by wanting to do what they were already doing.
I could also see Discord being released by Celestia because of the danger that Gralo had proven to be, and that she'd rather have a Chaotic Neutral as an Ally, rather than an enemy, just in case Discord's magic can't be drained away by others like Gralo.
Easily one of the most sensible statements I've ever heard in this fanbase. This is why I'm not a Trixie defender, nor a fan of the very concept of Discord redemption.
Heck, I haven't even seen that episode, for fear it will completely destroy my faith in the writers.
I have Canterlot Wedding for that already, thank you very much.
I had to skip everything you said about "Twilight's Kingdom", because I haven't seen it yet, I'm sorry