After the event, the ponified-changelings are revealed to have been basically oppressed by the queen, according to the changeling Butterscotch, which if it's true, means the only one that was Always Chaotic Evil was Chrysalis.
In the canon ending, the Elements of Harmony transform almost every changeling into a true pony permanently.
In the alternate ending, Twilight willingly becomes a changeling in order to take over the hive.
Apocalypse How: The Elements resort to this if there's a major disruption of harmony and no bearers. Twilight wonders how close to death they came during the first invasion. Under the current scale on that page, it's Planetary/Total Extinction.
Badass: Twilight already was one, even if her physical combat skills are initially lacking. By the time the story's over, she's become an experienced, battle-hardened killing machine over her many, many loops.
Batter Up: Twilight gets quite friendly with a baseball bat in one of the loops, which quickly becomes a favorite weapon of hers, to the point she affectionately calls it "Home Run". The name even gets engraved into the bat when the rest of the Mane 6 give it to her as a gift in her Thank-You party.
Beam-O-War: Twilight finds Celestia and Chrysalis engaged in one. Celestia will inevitably lose unless Twilight steps in.
Bittersweet Ending: Twilight manages to break the time loop and repel the changeling invasion with no major losses, but suffers immense psychological trauma in the process, which isn't made clear how well she will recover from.
Bloody Hilarious: The author didn't originally intend to make the story come off so comically, but Twilight's Deadpan Snarker narrative is both brilliantly in-character and stupendously hilarious enough to make several deaths entertaining to read. It helps that Twilight eventually becomes so desensitized to the idea of her death that she ends up being very nonchalant about it.
Body-Count Competition: Twilight gets into one with herself and becomes quite enthusiastic about beating her previous record of kills.
Twilight's initial confrontations with changelings result in her death multiple times. After looping enough times to predict exactly how a changeling will react in battle and gaining enough battle experience, she's the one dealing them instead.
Despair Event Horizon: Twilight's first "successful" loopnote Elements of Harmony contained, Crysalis dead, central Canterlot holding out, still alive after more than 31 hours ends with her throwing herself off a balcony and indulging in pointless violence and/or wish fufillment for the next several cycles.
The Ditherer: Twilight becomes a tragic case of this; spending months in the time loop leaves her with anxiety over the littlest choices once she gets out since she no longer has any way to go back and correct any mistakes she makes.
Driven to Suicide: Twilight, in the loop where she first discovers her friends will die if she doesn't prevent it, followed by Luna being killed in an ambush.
In the sequel, it's strongly implied that she would have ended up this way outside of the loop. Good things her friends intervened.
She gets to this point rather easily; an early loop (once she notices how she hasn't stayed dead) ends with her carefully positioning herself under a soon-to-be-falling wooden beam.
Duct Tape for Everything: During at least one killing spree, Twilight binds a changeling with duct tape before casually going over to it and smashing its brains in with HomeRun.
Emo Teen: Twilight apparently went though a phase of this when she was growing up. Spike is somewhat horrified when he thinks a time spell might be causing Twilight to repeat it.
Fantastic Aesop: After being killed by the Elements of Harmony, Twilight's reaction is that there's probably a decent friendship report somewhere in the fact that "misusing the power of friendship can not only hurt you, but can make every particle in your body explode at the same time". A valuable lesson for us all.
Chrysalis implies this is an overarching cause for the enmity between the two races. This racism becomes much more notorious once the changelings are permanently turned into ponies by the Elements of Harmony, resulting in some willing to take them in with others decrying and rejecting attempts to integrate them into pony society.
After her experiences with them, Twilight herself displays this racism quite strongly, and we can't blame her for it. She gets over it rather quickly though.
Fighting Your Friend: At one point Twilight gets brainwashed after being bitten by Chrysalis and is forced to attack Luna, who ends up killing Twilight in self-defense.
For Want of a Nail: Given the premise, Twilight, naturally, eventually indulges in this for a while, getting into some quite interesting and hilarious situations.
Friends with Benefits: Luna offers this to Twilight after inadvertently learning about their liaison in a previous loop.
Gilligan Cut: The story makes liberal use of these to show different loops, especially when dying in one results in Twilight correcting herself in the next one (or the relevant one several loops later).
Good Is Not Nice: After the Elements of Harmony permanently transform all changelings into ponies, Twilight reflects on the morality of this before pointing out that they're not called "the Elements of Niceness" after all.
A Good Way to Die: Subverted. Twilight delivers a scathing rant to Celestia when it's suggested her friends died in this way, and berates Celestia so harshly over her ignorance of death that it renders her speechless. This ends up coming back to haunt Twilight when Luna gets killed shortly afterwards, and her immense regret over her harsh words likely plays some small part in her suicide.
Gory Discretion Shot: For some of the more gruesome deaths. Averted for others, such as the time where Twilight describes her neck being snapped, or how a death was relatively good because she barely had time to feel her eyeballs boil.
"Groundhog Day" Loop: Resets every time Twilight dies to the point the initial "save-point" spell was cast, although without certain actions taken, the loop basically lasts around 3 hours before the Elements of Harmony destroy the world.
If You Kill Her, You Will Be Just Like Her: Averted. Celestia disappears rather than attacking Chrysalis when mocked over Luna's death, which Twilight explains is because she is better than this. Twilight then reminds Chrysalis that while this may be true for Celestia, it definitely isn't true for herself, before proceeding to cast a dark spell that results in an agonising and protracted death as a punishment.
Ignored Epiphany: Subverted. Twilight comes to believe that she's been approaching the situation incorrectly and that she's meant to bring about peace between ponies and changelings after the honest fun and good time she had with Chrysalis in the "tea party loop". Just as she resolves to do this, Chrysalis reappears moments after having left, nonchalantly states she changed her mind and cheerfully kills Twilight. Twilight promptly changes her mind about peace.
MacGyvering: Twilight eventually learns how to use common household items to put together high-grade explosive charges. After many tries of course. She puts these to good use to reduce a hallway and a large squad of changelings to a mess of molten rock and agonizing stragglers.
Neck Snap: Twilight ends up as a victim of this as part of her many deaths. Somewhat disturbingly, she carries on with her narration while describing the sensation of having her blood vessels snap and burst...
Noodle Implements: A weather vane. All that's mentioned is that Twilight seems to have enjoyed whatever Luna did with it...
Not in Front of the Parrot: Fluttershy talks about Twilight being gay to her animals while petsitting Rose's parrot. When she returns said parrot to her in the Ponyville marketplace, it escapes and ends up outing her to the entire town.
Pay Evil unto Evil: In one loop, Chrysalis maliciously and cruelly taunts Celestia by taking on the form of the recently-deceased Luna, prompting Celestia to vanish in a rage rather than taking revenge. Twilight states this is because Celestia is better than Chrysalis. Before leaving, she mentions she is not better than Chrysalis, then uses a dark magic spell to kill her while making sure she suffers the most excruciating pain imaginable until the very moment she dies.
Save Scumming: Twilight's key to victory, in classic Groundhog Day style.
Screw Yourself: A pony named Cloud Kicker all-but states to have done this with a changeling that was permanently transformed into a real version of herself due to the Elements of Harmony.
Shape Shifter Mode Lock: Not just any changeling, but almost every changeling. They become permanently locked into the form they had when the Elements of Harmony were used on Chrysalis. This is not merely a change in appearance; they were turned into a true pony in every single way, meaning no more Hive Mind or emotion eating.
Hard Reset ends with Twilight becoming one after the loop is finally broken. She has clearly received immense psychological trauma during their ordeal, to the point of suffering from nightmares, flashbacks, being terrified of making mistakes and becoming reclusive.
The first chapter of A Stitch In Time ensures that she's improving, though not totally recovered.
Sidetracked by the Analogy: When Twilight first enters the vault where the Elements are stored, she observes the "incalculable" wealth inside, only to correct herself and immediately start working out the best way to determine the value. She does manage to stop herself before she gets too distracted though.
Took a Level in Badass: Twilight takes several over the course of the story. Celestia help you if you're a changeling on her bad side.
We Meet Again: Twilight uses this when she first discovers Chrysalis has returned, before chiding herself for not coming up with anything more creative to say.
While Canterlot Burns: Twilight indulges in this after several loops and pursues some decidedly non-important things, ranging from trying on new dresses and attempting to determine the LD50* the median lethal dose; the amount of a substance required to kill 50% of a population and a standard measure of toxicity for donut frosting and sprinkles, to sleeping with Princess Luna.
Wrong Genre Savvy: Spike in one loop recognises there's some sort of time spell going on by noticing Twilight's different behaviour and attitude, but believes she's cast an age spell on herself instead of being stuck in a time loop.
Zerg Rush: Luna ends up being killed this way unless Twilight convinces her to fetch the mane cast.
A Stitch in Time provides examples of the following:
Badass Boast: Twilight actually delivers one of these. To Azalea, in fact.
Bad Date: Twilight, after a minor argument with one mare, ends up in retaliation dating another. It doesn't go well. Then again, given Twilight's experiences up to that point with mind-altering substances, it was inevitable. It leads to the Insult to Rocks moment below.
Blind Date: Applejack sets up Twilight and Azalea, and despite some early difficulties the two really hit it off.
Exact Words: After Twilight returns from her journey to the alternate universe, she tells a white lie to Azalea that it wasn't so bad. Azalea replies, "I'm glad. Tell me all about it." Because Twilight is still affected by Changeling venom, she is forced to tell the whole horrifying story, up to and including her alternate self becoming the Changeling Queen, until Azalea finally interrupts.
False Utopia: The antagonist has created one of these in her timeline to delude herself into believing that everything turned out fine after all. When the mask is torn away, she is not happy about it.
Fee Fi Faux Pas: Twilight expresses her distaste for Cloud Kicker's lifestyle, specifically "the way she’ll jump into bed with anypony with a pulse". Azalea's reaction to that tells her all she needs to know.
Game of Nerds: Twilight followed through on learning baseball. 'I really have been studying it since the girls gave me Home Run back at the party. If somepony had just told me it was ninety percent statistics I would have started following it sooner.'
Insult to Rocks: Twilight to a would-be date, Algae Bloom, who makes CloudKicker look like Rarity. Algae mentions briefly how her job at a pet store consists mainly of cleaning the "slimy plants" out of the tanks. Once Twilight has had enough of her, she launches into a lecture on cyanobacteria, describing its function in ecology, explaining why being described as pondscum wouldn't be as insulting as another mare would think, then telling Algae that she's not even worth its attention. And then she installs a new Berserk Button if Algae ever tries going too far on future dates.
Irony: Starswirl's letter mentions how Luna believed the Elements were a necessary counter to Celestia’s power in case she, unchecked, became a tyrant. "I have spent the last two decades appreciating the irony."
Mercy Kill: In what is perhaps the darkest moment of A Stitch In Time, Twilight discovers Luna. Under the effects of Queen!Twilight's mind-control venom, she has become little more than a Sex Slave. Twilight's traveling companion makes the decision to euthanize said pony.
My God, What Have I Done?: A few of these. Starts off with Twilight realising that she had, during the earlier story, started treating everyone as disposable tools. This includes herself.
Whenever I made some little mistake I’d cut my own throat open to jump to the next loop if I thought it would save me an hour.
Running Gag: Pinkie's inability to understand recursion, to the point where when she does get it right, Twilight reflexively starts to correct her. It's also a subtle hint that the individual using it isn't Pinkie Pie
Stable Time Loop: While in the alternate timeline, Twilight gives Starswirl the alias "Shooting Star", his daughter - Twilight's ancestor - who Celestia had told her about earlier. After returning to his time, Starswirl sends a letter telling Twilight that he named his daughter Shooting Star after the alias she "made up" for him.
Surprise Incest: Technically speaking. After sleeping with Luna in the original story in one timeline, Twilight is somewhat disturbed when she finds out she's descended from Luna and Star Swirl by about 40-50 generations, though Luna isn't bothered due to the very small degree of relativity this involves.
Kicky: Azalea mentioned that you two were going to Reuben’s deli for dinner this evening, right?
Twilight: Yeah, why?
Kicky Here’s a free piece of Azalea advice. When you get your sandwiches, give her your pickle.
Twilight: I don’t know what that means, but it doesn’t sound like something I’d be comfortable doing in public.
Kicky: That wasn’t a euphemism, Twilight. Azalea loves pickles. Offer her yours and you’ll score major marefriend points.
Walk on Water: Twilight and Azalea, thanks to a spell cast by Twilight.
Warts and All: Extending from how Twilight spoke highly of Starswirl in the show. When she meets him? Jerk. She eventually chews him out and leaves him in the lurch. This mirrors her attempt to date, too. Twilight even admits that had she not been on the other end regarding Azalea seeing her as larger than life and Twilight begging her to come back, she wouldn't have extended the same to Starswirl.
What the Hell, Hero?: During their intervention for Twilight, Rainbow Dash calls her out for letting the rest of them die when she'd already figured out a perfect victory plan, just so she could go back and take the opportunity to sleep with Luna. Twilight concedes the point, admitting that she treated the others, and herself, as disposable tools during the time loop.
"I’m Twilight Sparkle. You were scared of me before, and you have no idea how right you were."
Bittersweet Ending: Not in the main story, but the "bonus" chapter at the end. The character previously known as Changeling Twilight has existed for trillions of subjective years, and learned the value of forgiveness. She finally dies for good, as her universe ends, with her granddaughter by her side.
Bored With Insanity: Princess Sparkle claims this, almost by name. While she may be sane, that doesn't mean she isn't evil....
Cosmic Plaything: Twilight comes to consider herself this after having discovered Star Swirl's letter at the very beginning of the story. She's certainly got its attention, at least.
The multiverse hates me. It’s the only rational conclusion I can draw that fits all of the available data.
Cruel and Unusual Death: Everything that Alternate!Discord does to his Mane Six. It starts out tame enough, turning them into fruit, but then he literally wrings the blood out of Applejack, who he turned into an orange, and then drinks it. He then chops up the other five into chunks and then eats them. It should be noted all six of them are alive throughout the entire process and able to feel everything that's happening to them.
Earn Your Happy Ending: Twilight succeeds in saving the world, marries Azalea, starts a family, and ascends to become a princess.
Enemy Mine: Nightmare Moon. She is still shrewish and vicious and murderous, but she's quick to step into line with the protagonists when she realizes that her own existence is on the line.
Heel-Face Turn: Changeling Twilight. While still amoral to the extreme, she's no longer puppy-kicking evil. This is because she's had plenty of time to deal with it. And by deal with it, we mean plot her ultimate revenge.
Subjective millennia later, she learns the value of forgiveness and truly gets over it.
Twilight: The chemical substance, or the hallucinogenic?
Discord: Yes. Provided you don’t mix them up. Actually, especially when you mix them up.
Noodle Incident: Twilight and Luna discover some sort of plot during the epilogue that decidedly falls into this territory.
"But... but... enchanted spatula! We have to do something or the cultists will cross-pollinate with the mutant porcupines."
Save Scumming: Starswirl has an amulet that can bring him back five minutes if he's killed. Since it takes an hour to recharge, he can't use it with nearly the same wild abandon as Twilight did in the first story.
Time Abyss: Twilight's alternate, Queen Sparkle. She never escaped the time loop; after the events of A Stitch in Time, she is first driven insane and then driven sane again. By the end of the story, she has lived hundreds of trillions of subjective years until reality has degraded enough that time stops within her lifetime, ending the loop.
Wacky Cravings: Twilight ends up suffering from them in the epilogue. Azalea apparently went though a similar ordeal during her pregnancy.
The Reign of Queen Twilight Sparkle provides examples of the following:
Darker and Edgier: While a lot of the darker parts are implied or occur off page elsewhere in the trilogy, this story is not shy about showing what kind of horrors went down under Queen Twilight's rule.
Changing Lives provides examples of the following:
Retroactive Wish: When Cloud introduces Kicky to Lyra, her narration says that she "would give anything for something to interrupt this awkward moment." Cue Rose's parrot flying past, being chased by Fluttershy, saying, "Bwawk! Twilight Sparkle is a lesbian! Bwawk!" Cloud then wishes for a million bits to fall from the sky into her lap, but decides it must have been a one-time thing.
Noodle Incident: This fic explains nothing. The only reason for this thing to exist is because of a Noodle Incident in You Can Fight Fate that Twilight doesn't get to go on, and this fic explains none of it. Now we have to wonder about jam, ferrets, quiches, and how Luna will keep herself from telling Twilight about this.
Little Brother Is Watching: Once Twilight let Spike in on what was happening with the time loops, he's been reining in many of her more anti-social solutions.
Mental World: Chapter 11 takes place entirely within Twilight's mind …
Mind Probe: … because once the princesses learn that Twilight was on good terms with Cadence (who in this timeline was behind Luna's fall into evil), Luna mentally invades under the assumption that that's the only way to discover Twilight's true goals. Unfortunately for everyone, Twilight isn't actually a sleeper agent.
My Skull Runneth Over: The information Twilight receives from the Elements of Harmony severely overloads her brain, causing several deaths before Luna removes the memories.
Ripple-Effect-Proof Memory: Simultaneously subverted and played straight, in different ways. The story explores the premise of multiple intersectingtime loops, with the catch that only the first looper to die in a particular iteration will remember its events. At the same time, Twilight's unchanged memories of her original past become increasingly troublesome as the story progresses.
Time Crash: The story earns its "Reset Harder" title by having Luna and Twilight cause literally infinite damage to spacetime after Luna permanently kills Twilight. That deprives the time loop of its looper, causing a recursive failure. Fortunately, the Elements of Harmony are there to give them a second chance.
Trust Password: When Celestia hears that Twilight is a fellow time looper, she tells Twilight a password to unlock secret knowledge in Celestia's brain. When Twilight repeats the password to Celestia later on, she's paralyzed by a powerful spell, and Celestia immediately kills her after revealing that the "secret knowledge" is the rest of the password. It's repeating the ENTIRE combination that convinces Celestia of Twilight's story.