Some time before we met Twilight, she was given an assignment by Celestia to compile a report on the founding of Equestria. Celestia had been mysteriously absent from then on, prompting Twilight to address Luna regarding an unorthodox account of the founders. Luna panics and instructs Twilight to carefully dispose of the book she's discovered, though Twilight disregards this advice.
The following day, Twilight determines that Luna was trying to lead her to the old palace ruins in the Everfree Forest. She meets Luna there late that night, swears an oath to secrecy, and is then made privy to a number of secrets— not the least of which being that Celestia herself once went mad with power, and that NightMare Moon was Luna's desperate plan to save Equestria.
In this same time, the Cutie Mark Crusaders go digging in the Badlands. Sweetie Belle finds a rock (or perhaps it found her) that she believes enhances her magical prowess, and her disposition gradually degrades from bubbly to bratty.
It is discovered that Derpy, who is considered by most of the town to be an idiot, is actually just an absent-minded inventor with a vision problem. The most important ponies to her, in no particular order, are Dinky (her daughter), an unseen pony named 'The Doctor' (her husband), a pony named Dexter (who very clearly has a pathetic crush on her), and her estranged sister (about whom little is known). Derpy's most prized invention is a device that enables any kind of pony to have the abilities of all three races; a sort of alicorn exoskeleton. Unfortunately, like many of her other greatest inventions, it doesn't perform as expected. She believes she's got it working, but an unexplainable equipment failure cuts her test-run short.
After about 24 hours of exposure to the rock, Sweetie Belle is confrontational and rude, even to her own sister. Rarity forcibly removes the rock from Sweetie Belle's possession and, in the process of disposing of it, discovers its true form. Overwhelmed by its 'beauty', Rarity becomes obsessed with it as well— in a matter of hours it drives her to paranoia, racism, and violence.
Derpy, who has honed in on the device Sweetie Belle dug up using her ticker, enters Carousel Boutique as Rarity's corruption is at its peak. Derpy is able to intervene, quite possibly saving both unicorns' lives, and once Rarity is able to clear her head she deems the device ugly and undesirable, throwing it in the trash. Derpy recovers it quickly and takes it back to her home laboratory.
That night, Twilight returns to Luna to continue receiving education beyond what Celestia wanted to, or could ever hope to, teach her. Luna has shocking news; Celestia is actually engaged in failing peace talks with the griffon nation, and war is inevitable. It has been discovered that the griffons possess large quantities of Elements and that Equestria is not prepared to fight such a well-armed militia.
Even the Elements of Harmony won't be enough to engage the griffons. The only hope for Equestria is for Twilight to take on Luna's Element— the very thing that turned Luna into a monster — and maintain sanity while beating back most of the griffons on her own. Twilight understands the gravity of the situation and agrees that Luna's proposition is the only solution. She accepts the Element and is instantly put into a coma that lasts all night and most of the following day.
While in her coma, Twilight is forced to overcome a creature of darkness who threatens to take command of her mind and body. Despite the creature's best efforts, she is able to remember who she is and claim victory through memory of her friendship. Upon waking, she finds she's grown significantly in stature and her magical strength has been increased manyfold. Twilight meets both Dexter and a rather unpleasant voice in her head. She seems to be bothered by the concept that she is 'Celestia's Pet', a point that the voice harps on.
During the daytime portion of Twilight's struggle, Rainbow Dash and Pinkie Pie both independently discover that she has gone missing. Rainbow enlists AppleJack to help her search, and they decide to check the EverFree Forest, as it is the only place Rainbow hasn't yet looked. During their search, they come to the conclusion that Rarity's strange behavior and Twilight's absence can both be neatly explained by the return of Discord, and they quickly return to Twilight's library to contact Celestia via Spike. Celestia informs them that their concerns are unfounded and that the Elements of Harmony must meet in Canterlot immediately.
Celestia informs them of the same thing Luna told Twilight the previous night; the griffons are coming, and they are a force to be reckoned with. It is revealed that the Elements of Harmony are willing to disregard their own rules in dire circumstances, which means that Shining Armor can take Twilight's place as the Element of Magic. The five remaining ponies move quickly to a forward base established by the Royal Guard. Rainbow realizes that the Wonderbolts are there. Shining Armor is grief-stricken by Twilight's absence, and this appears to manifest in a hot-headed rage, but he is insistent on doing what he can to defend Equestria.
Twilight goes to bed and Luna sends a messenger from Canterlot to the military installation to inform Shining Armor that Twilight is alive and well. While she sleeps, Twilight dreams that she is a griffon with a horn. She speaks with herself briefly, and the griffon claims to be the king of all griffons, a position he earned through his efficacy on the battlefield. He is convinced that Celestia (known to griffons as a goddess called 'The White Mare') is responsible for destroying his childhood home and everyone he knew with a meteor shower. In his mind, this was a message from the gods to teach him of his divine destiny; the eradication of all living things. Twilight tells him that this is incorrect, to which he simply responds, 'help me'. The dream sequence is terminated by a meteor striking the Earth.
Shining Armor and the other Elements of Harmony receive the news of Twilight's wellness and are overjoyed. Shining Armor leaves them alone in his excitement and doesn't notice Rainbow sneaking out shortly thereafter. Rainbow derps her way into the Wonderbolts' tent with the intent of flying with them in the morning. She successfully convinces Spitfire to allow her to participate.
Late in the mission, the half of the Wonderbolts accompanying Rainbow are assaulted by a squad of griffons that includes Gilda. Rainbow acts quickly to help Soarin', successfully inflicting an injury on a griffon that prevents him from flying. Though she's initially satisfied by her victory, she quickly realizes the depravity of what she's done, and she decides she must prevent him from dying. She pursues him as quickly as she can, even performing a sonic rainboom to try to catch up, but there simply was not enough time for her to reach him before he struck the ice.
Rainbow is then pursued by the other griffons in the squadron, and she is able to out-maneuver all of them except one, which turns out to be Gilda. Gilda holds a grudge against Rainbow for the events of 'Griffon the Brush-Off', a grudge that has been intensified by the influence of an Element. Though she initially planned on killing Rainbow, the excitement of the chase reminded her of better times and she offers to spare Rainbow's life, giving her hero-status among griffons, if Rainbow agrees to kill one of the Elements of the Harmony (apparently an Element makes the concept of murdering one's friend much less bothersome). Rainbow refuses, at which point Gilda's rage flares and she prepares to perform an execution.
Rainbow is saved at the last moment by Fluttershy and Rarity, who are both uncharacteristically bold and tough. Gilda is beaten back and eventually retreats to the East to regroup. Rainbow was badly injured by Gilda, so Fluttershy and Rarity work together to carry her back to the base for medical attention. Before they can arrive, they are assaulted by yet another group of griffons, finding themselves too exhausted and insufficiently skilled in combat to take them all on. Twilight chooses this as the opportune moment to drop in and reveal her new form ("Say what you want about Twilight, the girl knows how to make an entrance." —Egophiliac), saving her friends and teleporting them back to the base.
Celestia is a unique combination of flabbergasted and enraged as she works out what had transpired the previous night, and she seems to instantly be aware of what has happened to Twilight, how, and by whose efforts it was made possible. Some short time later, Celestia briefs the Elements, teaching them how they must act in order to save Equestria. She drills Rainbow about where her loyalty lies before giving the others a series of tasks to perform.
It's revealed that Twilight's power is matched by her finesse, as she manages to fabricate solid metal from thin air, in much the same way that NightMare Moon prepared her own armor (how does Twilight know that, anyway?). After eating, the five regroup with Dash on the Eastern wall of the fort, and learn that she will be fine, though her wing will be too weak to allow her to fly for over a week. Twilight contemplates the curiosity of the ocean being frozen over, insisting that it's pointless from the griffons' perspective, and should be impossible anyway.
In the day since she visited Rarity's home, Derpy has retrofitted the Element into a magic amplifying device as the power source (weird that she figured that out so very fast, it seems like she has anachronistic insight. Somehow.). Completely unaware of modern events, she only wants to share and celebrate her success with Dexter, but in his love-induced nervousness he accidentally reveals details about the war that he was supposed to keep secret.
Derpy continues to have unusual knowledge about the topics at hoof, and she insists on directly aiding the war effort by combining the now-complete amplifier with the hopefully-complete transducer. She manages to operate the machine with competence, and as a reference of scale, it is mentioned that the amount of energy that the Element can supply in one second (50 millisols, by the way) is enough to 'flatten Ponyville'. Derpy also teaches us that the griffons are, in fact, already dead as a result of the Elements' influence, insisting that exterminating them is actually the most ethical course of action.
Derpy arrives on the scene quickly and, well, derps. She derps hard. She immediately determines that Twilight is a baddie (she was mauve!) and attacks, picking a fight with one of only two creatures under the Sun (and not encased in stone) that could overpower the transducer. She and Twilight do battle for a short time before they eventually figure out what happened and are thankfully able to stop before anyone is injured. Celestia witnessed the ordeal and was, again, shocked. She immediately made efforts to put Derpy under her direct supervision and power, though Derpy showed through her capacity to withhold pertinent information that Celestia does not have complete control. Derpy successfully volunteers herself to the war effort.
Twilight was tired from having just used more magic at once than she ever had, for a duration much longer than usual. During this weak moment, her friends were able to figure out that she had taken on an Element and are concerned about her. AppleJack lets fly an insensitive comment and that pushes Twilight over the edge. She blows up on her friends as her body involuntarily channels magic, terrifying them all. Only Fluttershy's kindness is able to restore Twilight's stability, and even so, it's unclear whether or not that will be enough in the long-run.
And that's right where we left off.
