Anachronic Order: The story starts at the beginning, skips to the middle, then continues on normally, only to have multiple flashbacks to the skipped segment.
Anxiety Dreams: Princess Celestia has dreams in which her sister becomes Nightmare Moon again and attacks her. It later leads to a mild misunderstanding when she wakes up in a hospital with lightning burns and Laser-Guided Amnesia.
Badass Teacher: Princess Celestia has fought in so many wars that her first action upon waking up in the burning wreckage of her student's experiment is to attack her with precise military moves, despite having multiple serous injuries, because she thought she was an enemy. She got better.
Bad Dreams: Princess Celestia keeps dreaming of her sister's transformation to her Nightmare Moon a millennium ago. She tries to hide it from Luna, with limited success.
Cain and Abel: A millennium ago, Princess Luna grew envious of all the attention that Princess Celestia got instead of her, she turned evil and attempted to eliminate her sister to bring about eternal night. Celestia was forced to fight back and banish her beloved sister to the moon. Luna's betrayal and the subsequent fight still haunt Celestia.
Celeb Crush: Twilight Sparkle had one on Princess Celestia. Of course, it helps when said celebrity is your teacher.
Celebrity Is Overrated: Princess Celestia realizes that it is her subject's expectations of her to be invincible that cause them to refuse to look at her directly when she is wounded and thus illustrating her fallibility. It unnerves her.
Child Prodigy: Twilight Sparkle was a magical and literary prodigy since the pony equivalent of six.
Complete Immortality: The Princesses, probably. Neither have aged in a millennium and Celestia survived being blown up with only a burn, a concussion, and a gash in her head. It is implied that Twilight Sparkle is heading this way as well.
The Confidant: Subverted. Princess Celestia briefly considers telling Twilight Sparkle about her extensive efforts to maintain her public image, but decides not to, as this would put an unnecessary burden on her.
Converse with the Unconscious: Twilight admits out loud that she loves Princess Celestia when she is cradling her broken body. Celestia not only does not hear this, but wakes up disoriented and attacks Twilight, not remembering who she is and thinking her an enemy. This does not help Twilight's Guilt Complex, and she later convinces herself that her words and the kisses she punctuated them with were the equivalent of rape and that she is a horrible pony.
Cool Teacher: Princess Celestia was this to Twilight Sparkle before she graduated.
Dreaming of Things to Come: Princess Celestia's graden dream could mean many things and is given different meanings by different characters. It could represent the growing relationship between Celestia and Twilight, the eventual success of Twilight's experiment, the coming immortality of Twilight, or any combination of the three.
Dream Walker: As expected of the Alicorn of the Night, Princess Luna is able to explore and manipulate others' dreams.
Dude, She's Like, in a Coma!: Much of Twilight’s angst comes from this (along with general PTSD and guilt over blowing her up in the first place), as her reaction to Celestia’s seemingly dead body is to kiss the Princess repeatedly. Not only is it a lot more icky than any ‘true loves kiss’ (as Celestia is covered in blood at the time), Twilight later convinces herself that it was some sort of rape and she’s an awful pony for doing it.
Dying Declaration of Love: Twilight finally confesses her love to Princess Celestia after the latter had been blown up in her experiment.
Emperor Scientist: Though she doesn't seem to have much time for it anymore and is somewhat unfamiliar with a modern lab setup, Celestia is mentioned to have been quite the scholar and scientist in her younger days. When she attends Twilight’s first test of her new theories she has to resist the urge to make suggestions unless asked, reminding herself that this is Twilight’s project.
Environmental Symbolism: Princess Celestia's Mental World symbolizes her mental state, and so the environment changes to conform to and symbolize aspects of her current thoughts. Also, in her garden dream, the plains represent life and the horizon represents death. There is much more symbolism in that dream than is possible to detail here.
The Four Loves: Celestia and Luna disagree on what Celestia feels for Twilight Sparkle. Celestia insists that it is Phileo, Luna is sure that it is Eros. It is this argument that accidentally triggers Celestia's Superpowered Evil Side.
Gaussian Girl: When Twilight Sparkle casts an illusion spell on Princess Celestia to hide her burns, it shows as Twilight Sparkle sees her. The effect is equivalent to a Gaussian blur.
God Empress: The perception of Celestia as this is the source of much of her problems. She realizes from the horror shown to the very concept of her being injured that she IS her subjects state, religion and piece of mind, and that the idea of her being mortal and fallible terrifies them.
Going Critical: Twilight's experiment, which is the magical equivalent of a nuclear reactor, does this just before it explodes.
Green-Eyed Monster: Princess Luna seems to be very susceptible to this, even after her Superpowered Evil Side was destroyed. She becomes jealous of Twilight Sparkle's relationship with her sister, fearing that the unicorn was taking her spot in Celestia's heart. She got better after she realized that Celestia's love for Twilight was not platonic.
Hot Scientist: The other researchers certainly have this opinion of Twilight Sparkle.
How Dare You Die on Me!: Twilight has this sort of reaction when she thinks Celestia had died trying to prevent her experiment from cascading.
How We Got Here: Sort of. There is a brief prelude, then it skips to the hospital. The story then proceeds from there, with frequent flashbacks to the missing segment of time.
I Can Still Fight: One serious early complication of Celestia's head injury is her recurring belief that she's been attacked, and her attempts to fight back. Her reaction to Twilight Sparkle trying to get her some much needed medical help is to try and kill her in her disorientation, which apart from delaying her treatment was very likely to cause her further injury.
Celestia sees even more potential, realizing that it is the same energy that provides her powers and immortality. Her first thought is the possibility of using it on Twilight, chronologically the earliest hint that Celestia's feelings are far stronger than she's letting on.
Princess Celestia wakes up in the hospital with bad burns, an inability to use magic, and no memory of anything after her sister visiting her room that morning, including what happened in Twilight Sparkle'sdisastrousexperiment. Thanks in part to her Dark and Troubled Past and Anxiety Dreams about nightmare Moon returning, Celestia assumes that her sister turned evil again and attacked her. This both illustrates Princess Celestia' love for Twilight, as she immediately sets out to find her and causes the Princess great guilt for mistrusting her sister when she finds out what really happened.
The Princess later has a minor freak-out the night after her accident when she wakes up next to Twilight Sparkle and does not remember what happened the entire day before, meaning that the amnesia extended to both before and after the explosion.
Love Hurts: Through convoluted logic and a healthy smattering of guilt for the explosion that hurt Princess Celestia, Twilight Sparkle convinces herself that being in love with Princess Celestia is an extraordinarily cruel act of manipulative treachery. She reacts accordingly. Celestia on the other hand feels love is something she cannot entertain, as her role as Princess precludes any such selfishness and any relationship she has is tainted by power imbalances.
Made of Iron: Ponies are normally tough, but holy wow Celestia. Her injuries from the accident seem pretty bad, but when the true extent of it becomes clear it’s easy to see why people are so surprised that she didn't instantly become chunky salsa. Later it backfires, as her metabolism is just too tough for sedation and pain killers to work properly.
Manipulative Bastard: Luna thinks Celestia's this, and though she has good intentions it's easy to see why.
Mayfly-December Romance: An immortal Alicorn and a powerful but mortal unicorn though there is mild foreshadowing that implies that Twilight might attain immortality as well.
Matriarchy: Although the world is generally pretty gender equal, the two rulers of Equestria are both female.
Monumental View: Princess Celestia's room has one. She can see the entire princessdom, including Ponyville.
My Sister Is Off Limits: Subverted. Princess Luna She actually gives her a version of this speech in which she asks Twilight not to steal her sister away from her and displays the occasional bout of jealousy, but is eventually thrilled to realize that her sister really does loves Twilight Sparkle and fights to get them together.
Not Himself: Although it has never been stated outright, it is implied by Twilight Sparkle and Princess Luna that Princess Celestia was acting extremely Out of Character after being blown up, up to and including attacking both of them.
Celestia slightly plays this, as she performs some pretty impressive mental acrobatics to convince herself that her love for Twilight is simple affection, and that Twilight's love is a simple childish crush.
Twilight Sparkle believes her crush on Celestia is completely unrequited and is simply oblivious to the admiring gazes from many of her assistants, especially Peppermint Jam.
Overshadowed by Awesome: Twilight Sparkle is one of the most powerful unicorns to have ever existed and holds one of the Elements of Harmony, the most powerful magical artifacts to exist. She is a genius who is pioneering an entire new branch of magical theory, and her quick notes would be the equivalent of a doctoral dissertation for any other pony. Celestia is an immortal Alicorn god empress with control over the sun and wielded all six Elements of Harmony into battle before. No contest.
Also a big part of Luna’s character. Though she’s empathic, kind, powerful, intelligent and regal, her subjects still consider her a poor second place to her sister and Celestia runs rings around her in any emotional confrontation. Luna’s search for self respect and her attempts to find the slightest flaw in her sister’s near perfect composure becomes the source of much of the fic's plot.
Pair the Smart Ones: A genius who revolutionized magical theory with her discoveries and her teacher in a romantic entanglement.
The Professor: Twilight Sparkle is steadily moving in this direction.
Queer Romance: The story is slowly but steadily heading this way.
Reality Is Unrealistic: Celestia’s sudden revival from death seems rather dramatic, but people can quite easily be unconscious with their eyes open and Twilight herself admits that she is too over-stressed and untrained to effectively determine whether Celestia had a pulse or not.
Sanity Slippage: The entire story has been a very subtle one for Princess Celestia, dropping hints about her emotional instability and constant compulsive maintenance of her composure that are only noticed upon re-reading the entire fic. It eventually results in the release of her Superpowered Evil Side into her Mental World after Princess Luna keeps insisting on her revealing her true self and she refuses to.
Stop Worshipping Me : As normal Celestia has to throw a bit of this around, especially to Peppermint Jam and even to Twilight when she continues to call her Princess.
Student Teacher Romance: Averted by occurring several years after the series ends and upgrading Celestia's and Twilight's relationship to a sort of mentoring friendship. Celestia does attempt to use this as reason not to admit her feelings but Luna points out that this simply insults Twilight's status as a mature adult.
Superpowered Evil Side: Both Princesses have one. Luna's was defeated years ago by the Elements of Harmony. Celestia's is accidentally triggered by Luna telling her to give up her precious composure and admit her feelings for Twilight while in Celestia's dreamworld, which is affected by the whims of her emotions. Ooops.
Surpassed The Teacher: Twilight is now a specialist who knows more about the magic of friendship than Celestia ever did, to the point that she is devising a system to generate power from Harmony.
The Fog of Ages: During her dream sequence Celestia is reminded that each of the colors in her hair is so she would never forget someone who was once important to her…and she can't remember any of their names.
You Wake Up in a Room: Princess Celestia wakes up in a hospital room after Twilight Sparkle's experimentexplodes. Thanks to her Trauma-Induced Amnesia, her last memory is her sister entering her room that morning, she is badly burned, and using magic is painful due to a horn injury. She assumes the worst, that her sister turned into Nightmare Moon again and attacked her, and immediately flees the room looking for Twilight Sparkle. It is one of the earliest indications of her love for the unicorn.
What the Hell, Hero?: Celestia decides early on that she cannot romance Twilight Sparkle, but her interactions with the mare are so flirtatious that even Twilight is forced to wonder if she’s doing it on purpose. Luna quite rightly calls her out on this.
Webcomic Time: The story has so far taken up two days and three nights. The writing of the story has taken over a year.
White Mask of Doom: Princess Celestia's Superpowered Evil Side sports one. It looks exactly like her face with her usual serene smile over her face, except that you can see her eyes through the eye-holes and they are red and tired. The mask cracks when the Superpowered Evil Side is released. The mask represents Celestia's composure. All her emotions were buried underneath it and have resulted in a monster.