In case you need a refresher, here's a recap of the story thus far...
Act I: The Broken Soldier
An attempt to create a permanent doorway between Ponyville and Canterlot was interrupted when the Elements of Harmony intervened, connecting the door to another world. They pulled a man named David Corban from this world, turning him into a pony. Unsure whether of not the ponies were hostile, David claimed amnesia. Twilight Sparkle, feeling responsible for his predicament, took him in and gave him the name Midnight Star, after his midnight blue coat and the star shaped white patch on his forehead.
The truth was revealed when a surprise party sent him into a flashback, injuring Pinkie, knocking out Rarity, and launching a fireball at Twilight using his Seal, a runic circle that allows him to tap into elemental magic. After, he explained how he was once a part of an elite military unit called the Mage Guard, a unit of people imbued with a demon's blood. He told them of how, upon learning his love, Sarah, was pregnant, the two deserted. After their child, Tiffany, was born he attempted to exercise his demon. When he succeed, the demon took form, butchering his wife and child in front of him and leaving him alive to suffer for “imprisoning a god”.
After some time, Midnight began to adjust to his new life, even entering a relationship with Twilight. While defending the town from an attacking horde of monsters, lead by one that blinded Scootaloo (which led Rainbow Dash to adopt the filly) months prior, Midnight was gifted with the Element of the Guardian, one four Elements of Order. It was thanks to this element that he was able to defeat the monsters.
The act ended with Princess Celestia informing him that the emergence of the Elements of Order is a bad omen, as every time they appear, the world in plunged into darkness. In response, she forms the Dawn Shield, an organization comprised of the Elements of Order, when they emerge, and the Elements of Harmony. She tasks Midnight to train Twilight and her friends, along with a handful of others, to deal with this coming threat.
Act I Interludes
The Big Day: Midnight's and Twilight's wedding and the reveal that Twilight was pregnant.
The Blue Bandit: Blue Streak, a thief with a Robin Hood complex is captured by Dawn Shield and given the choice to go to prison or lend his talents to them. He chooses the later.
Act II: The Greatest Crusade
After an incident with a roc trying to eat them, the Cutie Mark Crusaders found themselves in a strange underground facility that predated the Princesses. The technology level of the facility suggested that ponies were much more advanced at one point, as shown by an advanced leg mounted computer acquired by Sweetie. Unfortunately, the facility was littered with the bones of the ponies that once worked there.
After navigating the facility, the stumbled across a laboratory. It was discovered that the facility was run by Doctor Bright Field, the son of Queen Clover Field, aka Clover the Clever. It was established to for the purpose of genetically engineering a weapon to use against Discord.
While Applebloom and Sweetie searched the lab for anything useful, Scootaloo, feeling useless with her blindness, decides to take a nap on a bed in the lab. When Applebloom discovered the power switch, though, the bed locked Scootaloo in and closed around her. It then injected something into the back of her head, giving her the ability to “see” magic all around her.
It was shortly after this that ravenous creatures, ones bred in the facility that were sabotaged by a pony looking to garner favor with Discord, woke up from their centuries long stasis. The three barely escaped the facility with their lives where they met up with Midnight as he was searching for them.
When the creatures emerged, pursuing their prey, the CMC stood by Midnight, ready to fight and die if need be. Their willingness to protect Equestria triggered the other three Elements of Order to appear.
Sweetie Belle, always using her head and thinking things through, represented Knowledge.
Applebloom, not only having the strength to tear a foot thick security door from its hinges but also the emotional strength to always press on, supporting her friends, represented Strength.
Scootaloo, who was always moving forward, even when she was scared, and even leading the monsters away from her friends, represented Courage.
With the Elements of order gathered, the four used unleashed their power on the creatures, destroying them.
Afterwards, Celestia asked the fillies if they would be willing to join Dawn Shield as well. Despite the concerns of their families, the three agreed.
Act II Interludes
Young Love I, II, and III: Sweetie Belle and Spike have their first date along with Scootaloo and Storm Feather, a pegasus colt from Canterlot living with his aunts, Lyra and Bonbon. Applebloom, feeling left out, lets her emotions get the better of her and kisses Midnight, whom she's had a crush on for some time. When she came to her senses, she ran off in horror into the Everfree. There, she found an old, ruined chapel. Inside, she met the ghost, Nightshade, a twelve year old filly that had been dead for over 1300 years. Nightshade, happy that somepony could see her and not run in fear, agreed to help Applebloom convince Twilight and Midnight to let her join their herd when she gets old enough.
An Elegant Engagement: Rarity and Virgil, the high class, pony raised diamond dog, go to his parents' home to announce their engagement.
Act III: Shadows of the Past
After finding Midnight's human brother, Jacob, in Equestria, it is revealed that Midnight's old nation is preparing to invade Equestria using a device simply called, “The Gate”. The Gate was an interdenominational portal that the nation of Korda used to steal resources from other worlds. He tells everyone that Equestria was discovered several months before Midnight's arrival, leading Twilight to hypothesize that the Elements of Harmony sensed what was about to happen, and pulled Midnight there for the purpose of protecting them.
Jacob, being an engineer and runesmith, embedded runes on the ponies to help them fight. Runes are similar to Seals with the exception that each rune is only a single spell, and that non-humans could use them (Seals being usable only by humans).
While training for the coming battle, Dawn Shield was granted thirty of Celestia's finest elite guard, as well as a squad of Tigerian mercenaries led by Zhatka, the cousin of a hind-legless tigerian inventor they met in Canterlot, named Shiro (I regret nothing).
Eventually, the day of the invasion came. While the others fought the human army, Twilight and Midnight snuck through the portal to Midnight's old world with the intent of destroying the facility so they could never again threaten Equestria.
On the Equestrian side, after witnessing what she believed to be Scootaloo's death, Rainbow Dash became enraged. The Elements of Harmony and Order suddenly appeared of their own free will, reacting with the ponies' runes, transforming them into full fledged seals. Rainbow's new seal used her rage to summon Quetzalcoatl, the dragon spirit of the air seal. The dragon god's rage decimated the enemy. The survivors that couldn't retreat back through the portal, either ran away into the Equestrian wilderness, or surrendered to Dawn Shield and were taken into custody.
After battling one of his former Mage Shield comrades, the two made their way back, where they were confronted by Nag-Ta, the demon that once dwelt within Midnight. The demon dragged the former human back to Equestria where he began toying with Dawn Shield.
When Aurora, after running out of the town shelter, tries to help, Nag-Ta grabs her and tries to kill her. Before he could, though, Lyra showed up, following after the filly, and used an enchanted arrow to blow off the demon's arm. Enraged, he moves to just kill everyone. It was then that something happened within Aurora. She began pulling in magic from all around, pooling in one powerful orb of raw magic that she unleashed at Nag-Ta, utterly destroying him.
The day after the battle, the first scavengers finally worked up the courage to move in. One, a coyote, ventured deeper into the still tainted battlefield, finding a particularly attractive morsel, Nag-Ta's severed arm. After consuming it, the demon's blood allowed Nag-Ta's essence to possess the wild dog, ensuring the demon's return.
Afterwards, Rarity and Virgil decided they wanted children, and three months later she was just starting to show. A visit to the doctor reveals that the spell Twilight cast to match their reproductive systems – they had decided to have pups in order to start rebuilding the Silverpaw clan – was a bit overpowered causing Rarity to become pregnant not with one pup but three.
Relationships had also taken a jump as not only did Storm propose to Scootaloo, but Jacob and Pinkie hooked up as well.
The act ended with coyote Nag-Ta brutally murdering a small filly, skinning her alive and wearing her skin. This act somehow caused a dark magic artifact to appear, a black metal claw on his left forepaw. With it, he murders the child's mother, ripping her soul from her body and imprisoning it within the artifact where it continued to feed him power.
Act III Interludes
Bounus Chapter:
A Story by Aurora Star: Much daww.
The Filly by the Roadside
The story of how Rainbow Dash found Scootaloo unconscious near Ponyville, with no memory save a single name; Cloe.
Birds of a Feather
Fluttershy accompanies Blue Streak to see his sister, Valara, a one-winged griffin that runs an orphanage in Fillydelphia.
Act IV
Sweetie Belle and Spike are married in the traditional dragon fashion of 'Soul Binding'. This results in Spike developing a pony-like mane and Sweetie developing dragon-like eyes and teeth.
Nightshade, seeing Applebloom's desperation to win Midnight's heart, offers a radical idea, to allow Nightshade control of Applebloom's body.
Applejack approached Luna, having stayed at the Apple family farm in order to announce her and Big Mac's relationship, about her concerns for her sister and who she believed was an imaginary friend. When Luna recognized the name of Nightshade as the same spirit that turned her to Nightmare Moon, they attempted to stop Nightshade, but failed.
After abducting Midnight and Twilight, Nightshade reveals her true reasoning behind her actions. She told Midnight how she was raped and murdered by Celestia's Student long ago, and how Celestia simply covered it up. Seeing the Princess of the Sun as a heartless dictator, she wishes to replace her with her sister. Throughout it all, she insisted that Midnight and Twilight give Applebloom a chance and not to blame her for what Nightshade influenced her to do.
When Nightshade met with Celestia under the impression of negotiations, Nightshade used Applebloom's great strength to attempt to assassinate her, however when Midnight escaped and pushed her out of the way, he was struck with the attack.
Thinking she killed Midnight, Nightshade ran into the forest, where she eventually released Applebloom out of guilt. Applebloom, blaming herself, ran away, deeper into the forest.
Applebloom made her way through the Everfree Forest where she eventually encountered Midnight Storm, and half dragon pony who was the result of illegal experimentation. The dragon-pony lead Applebloom to a small mining town where she lived.
Applebloom had only been there for a couple days when, as she tried to get a drink at the local tavern, a griffin came in. He tried to force her to sleep with him, but she shot him down. Insulted, the griffin and several friends waited for her to leave. They tried to 'make an example' of her, but only ended up getting beaten quite severely.
Several more days passed before she learned that the griffin she beat was the son of the leader of an outlaw mercenary group when they came to the town looking for payback. After a hard fought battle, the merc commander was defeated.
Knowing that her actions would draw the attentions of the friends and family she abandoned, she resigned herself to a drink as she awaited their arrival.
In a dark cavern, though, Nag-Ta began preparations for an unknown plot. After forcing a stallion watch the brutal torture and murder of his wife and foal, he was placed above a mirror pool, corrupted by the demon's blood. Instead of producing cloned of the stallions physical body, it created grotesque reflection of his tormented soul.
Act V
Beginning just after Applebloom ran away in Act IV, Storm Feather revealed himself as a changeling. Force feeding on Twilight and Fluttershy for power, he used a powerful spell to save Midnight by turning back time on his injuries.
He was arrested, along with Scootaloo and Sweetie Belle who kept the others from stopping what they saw as a changeling attack. Upon interrogation, he revealed that he was, in fact, a part of the invasion of Canterlot at the age of ten. When he was thrown from the city, though, he was discovered by Lyra and Bonbon who took him in.
He revealed that the two ponies had experience dealing with changelings and had helped a great many of them fit in with Equestrian society. He also revealed that he stole Twilight's and Fluttershy's love because it was more powerful than given love, though it’s addicting and corrupting nature meant he would have to be quarantined for several days.
As Twilight lay recovering, Shining Armor and Cadence came to visit and make an announcement; they were seeing another mare. While initially upset, Twilight asked to speak to this mare. The mare, as it turned out, was Sunset Shimmer, a student that had vanished nearly a decade ago. After speaking to her, she finally gave her blessing (and mandatory warning).
Upon his release, he was convinced that, having just saved the life of a hero, this would be the best time to reveal himself and hopefully show the ponies of Equestria that there are peaceful changelings. Unfortunately, this also alerted his existence to the changeling queen.
The queen lead a surprise attack to retrieve Storm, her son. However, the queen had expected the townsponies to be as soft and weak as those in Canterlot. Instead, she learned that living beside the most dangerous forest in Equestria hardened them.
Not only did the ponies of Ponyville fight back, the soldiers of Dawn Shield also proved more formidable than expected. However, it was the appearance of Scootaloo that ended the invasion. The queen, calling the blind pegasus 'Pan', claimed to be 'Cloe', the only name Scootaloo remembered from before she arrived in Ponyville.
After the battle, they received word of another fight in a town on the other side of the Everfree. Recognizing the mare described as Applebloom, Midnight and Twilight went to find her.
After finding her and filling her in on what she missed, Twilight made an offer; she would give Applebloom one chance to make a herd work. With the chance to finally find the love she desired for so long, Applebloom returned to Ponyville.
However, Nag-Ta continued his machinations by convincing a distraught Nightshade that he could help her. He tricked her into undergoing a ritual that would let her not simply possess a body, but truly inhabit it as a living being once again. However, the 'evil creature' was not evil, but Midnight Storm. Now, not only did Nightshade have the new guilt of stealing an innocent being's body, but she was bound to Nag-Ta.
Now forced to serve another, she was sent to the Crystal Caverns beneath Canterlot to find a mysterious ally for her new master.