Equestria went to war against the Zebra Empire and a megaspell exchange devastated the world. Some predicted the risk and built the Stables, bomb shelters that could sustain small populations for generations. After closing shut on the day of the megaspell exchange, the Stables eventually reopened on a bleak, irradiated landscape, except Stable 2, which did not open for two centuries...
A PipBuck is a hoof-mounted computer with some useful features like an eye-projected HUD, wall-penetrating hostile detection, a targeting spell that briefly speeds time perception, data management, and a location tag so everyone in a group that shares their tags' IDs can find each other. Littlepip, the protagonist and a Stable 2 native, has a PipBuck cutie mark. Since everyone in Stable 2 has a PipBuck, and the only magic she can use is telekinesis (which every unicorn can use), she finds herself underwhelming.
Velvet Remedy left a message near the door asking that no one try to find her. Littlepip continues anyway, doubtful that a hardly useful PipBuck technician's apprentice contaminated by the Outside would be allowed back in without her. Slavers capture Littlepip just outside a withered Sweet Apple Acres and die fighting raiders. Littlepip and fellow captive Monterey Jack avoid the fight. Monterey Jack tries to rob Littlepip, but Littlepip outmaneuvers him, sends him on his way, and holes up in the abandoned Carousel Boutique.
Littlepip meets a sprite-bot, a little flying robot ball playing cheery broadcasted music. They're a common sight in the Wasteland. Someone calling themself Watcher has hacked into the sprite-bots and can use them as cameras and phones. Watcher recommends that Littlepip get a good weapon, some armor, friends, and the Wasteland Survival Guide. Watcher says the Guide is in Ponyville's library. Littlepip goes to the library and finds that the raiders have made it their home, and they brutalize and rape their captives. She kills all the raiders and frees their surviving captives, including a wall-eyed pegasus who's apparently a zombie, and she dons some of their armor while cleaning out the library.
Littlepip raids an Ironshod Firearms building and procures Little Macintosh, an excellent unique pistol that was a gift from Applejack. Watcher tells her she should find her virtue, the principle she'll stand by no matter what, and that there's a special set of virtues--loyalty, laughter, generosity, honesty, kindness, and magic--that she should keep an eye out for. A charismatic stallion overrides the sprite-bots' music signal to deliver a speech about building a new Equestria. Littlepip tries to defend a caravan from a pegasus who she thinks is a raider (since he shot her) while he tries to defend the caravan from Littlepip, who he thinks is a raider since she's wearing raider armor. The misunderstanding ends when she shouts, "Shoot at me all you want, but if you attack that family, I will end you!" and passes out from her wounds.
The pegasus, Calamity, apologizes to Littlepip once she regains consciousness. They're in New Appleloosa, a town built of train cars. One of the shops is a delivery service run by Ditzy Doo, the derpy captive Littlepip saved from raiders. She was caught at the edge of a balefire bomb's blast when the war ended and became a ghoul. A skilled telekinetic offers to teach Littlepip to use her only magic well if she exterminates some monsters in Stable 24. Calamity joins her on the mission as a further apology. Stable 24 was subject to social tampering by Stable-Tec; they emphasized stallions' abilities with revised history and chauvinistic propaganda. Everyone in the Stable died from cat-snakes with wasp-like ovipositors known as Chimeras, created when a unicorn filly's magic epiphany accidentally fused three nearby animals. A monster lays eggs in Calamity and Littlepip braves an atrium full of the monsters with a one-use personal invisibility device (called a StealthBuck) to retrieve a cure the Stable ponies made in their last days. With Calamity saved, Littlepip leaves dynamite throughout the Stable and sets one bundle off to collapse the structure.
Littlepip plays a recording from Stable 24's Overstallion's office. It's Stable-Tec Vice-President Scootaloo, who reveals that the Stables have social experiments running in them in an effort to find a better form of society that can avoid pre-war Equestria's problems. New Appleloosans say the "build a new Equestria" stallion is Red Eye. A radio in New Appleloosa plays DJ Pon3 Radio, mainly music with occasional news segments, the latest one reporting Littlepip's killing the Ponyville raiders and rescuing Ditzy. Littlepip learns that Appleloosa is a slaver town and it trades non-slave goods with New Appleloosa. Calamity gives her a Party-Time Mint-Al to boost her intelligence when she tries to convince some train ponies to attempt to rescue the slaves at Appleloosa. With the drug's help, the job is easy. While Calamity waits as a sniper for when things get hot, Littlepip sneaks into Appleloosa and finds an Applejack Statuette with "Be Strong!" engraved on the base. When she picks it up, she feels stronger and more confident. She's discovered by some isolated slavers and kills them. Then she finds Velvet Remedy singing for a crowd of slavers.
The slavers catch on to Littlepip's presence and she loses them long enough to talk to Velvet in Velvet's room. Velvet is actually working for the slavers willingly, mainly medically helping the slaves as much as she can. Littlepip sells Velvet on the rescue attempt since there's backup and a train waiting to take everyone to safety. Velvet and Littlepip sneak to the slaves' holding cells and Littlepip starts to pick the locks. An alicorn walks up and tries to kill our heroes, so Littlepip drops a boxcar on her.
The slavers attack the fleeing train, so Calamity puts the freed slaves on the caboose and detaches it, leaving the slavers with the heroes and train ponies. The slavers kill the train ponies, but by this time they've pulled the train over a mountain pass and it's going downhill. After the heroes kill the slavers, Calamity takes Velvet down to safety and then catches Littlepip as the train careens off a turn in the train track. Littlepip convinces Watcher to send the New Appleloosans to help the slaves stuck on the caboose.
Littlepip has trouble cracking a safe in a crashed skywagon, so she pops a Party-Time Mint-Al and unlocks it easily. When asked why there aren't more pegasi around, Calmity reveals that when the megaspells fell the pegasi closed the clouds and continued civilization away from the surface in the Grand Pegasus Enclave. Hence the constantly overcast sky. Watcher explains that they sent Littlepip to the library hoping she would help the captives. Littlepip has seen some billboards for "Ministries", and asks Watcher what those were. Watcher says Celestia was protective of a group of six heroes and abdicated when the war got bad. Then Luna, who saw them as her saviours instead of as her children, put them in charge of their own government divisions. Our heroes spend the night at a rock farm whose only occupant is a Pinkie Pie-obsessed cheery filly named Pinkie Bell. Turns out she accidentally led ponies running an unpaid protection racket to her family and they were murdered slowly as an example to the area's rock farmers while she watched. Then she tried to be like Pinkie Pie, always happy, by imitating Pinkie's mannerisms, building a Pinkie Pie musuem, changing her name from Silver Bell to Pinkie Bell, painting her coat pink, and sawing off her own horn. Velvet confronts her about it.
Silver Bell had some fireworks ready for the museum-collection-complete party: an undetonated balefire bomb. Some New Appleloosans come over. Ditzy Doo takes Silver Bell with her, and the others take the balefire bomb. Our heroes are banned from New Appleloosa for making them enemies of Appleloosa. The griffin Gawdyna Grimfeathers sends Littlepip and Calamity to steal Deadeyes's ledger from a prison-turned-fort. Deadeyes is said to be working for a mysterious Mr. Topaz. Gawd keeps Velvet as collateral. Sweetie Belle sang at the prison to keep up morale, and in a safe containing some of her belongings, Littlepip finds a Rarity statuette with "Be Unwavering!" engraved on the base. It replenishes some of her almost-drained magical energy--she'd been overusing her horn.
Littlepip steals the ledger with the aid of a StealthBuck she found. She hears Deadeyes telling his guards to make sure Red Eye's slavers, who are coming to attack the fort, get inside. Our heroes reunite, Gawd gets the ledger, and it turn out Deadeyes was running that protection racket on the rock farmers and ordered the murders. Gawd wants him dead.
Gawd tries to hire Littlepip to assassinate Deadeyes. She's up for the job, though Velvet finds it distasteful. Littlepip plans to leave Gawd in charge of the fort, hoping it will some day be a functioning town. When Littlepip returns to the fort, Deadeyes hires her to assassinate Gawd. She sells him on a plan: have a Velvet Remedy concert during which she would shoot Gawd and miss Deadeyes' head, putting a bullet in the table, leaving everyone to think the slavers tried to kill both of the local leaders. At the concert, Deadeyes tells Littlepip that the stage has explosives in it that one of his employees will trigger if Littlepip shoots anywhere else than where they agreed. Littlepip telekinetically pushes Velvet backstage and then kills Deadeyes and puts a bullet next to Gawd. Slavers attack the fort early. Our heroes investigate a vault and find Mr. Topaz, a dragon who set up Deadeyes's enterprise so he could feast on the thugs and then feast on the attacking slavers before his hundred year sleep. Littlepip and Calamity become dragon slayers.
Littlepip uses a memory orb, which stores the recorded full sensory experiences of a donor, to see Fluttershy telling her ministry they have a new project she thinks will end the war. Once someone touches a memory orb with their magic, it blocks out their own senses and bodily control, and they can't come out until it's over. Our heroes head to Manehattan, where Littlepip hopes to meet DJ Pon-3 and get information from her before taking on Red Eye's slaver empire. They find the Sky Bandit, a pre-war pegasus-pulled bus that, given the right component, could fly them around the Wasteland. When asked what his cutie mark is--he's been wearing a battle saddle covering it--Calamity shows that he's been branded in the shape of Rainbow Dash's cutie mark over his own. It's what the Grand Pegasus Enclave does to those who abandon them to help the surface. Three alicorns turn up and attack the heroes.
A pony in powered armor turns up and kills two of the alicorns with a machine gun that shoots grenades. The third gets a force field up in time and breaks the power armor. Littlepip pops a Party-Time Mint-Al, wraps her telekinesis around a memory orb, and floats it surreptitiously up to the alicorn like it's a grenade. The alicorn directly picks it up with her telekinesis to toss the "grenade" away, is pulled into the memory, and goes limp as her shield drops. One easily killed alicorn later, Littlepip talks to the powered armor pony, SteelHooves. His armor is self-repairing but its spell matrix crashed. Littlepip agrees to fix it, but she needs a tool she doesn't have. SteelHooves says the tool she needs should be in the nearby Stable 29. They enter the Stable and discover that it was run by one of the Crusader Maneframes, the world's most powerful supercomputers; only three were ever made. It killed everyone in the Stable since the water talisman was damaged and its programming made it keep reducing the population to keep it within the amounts the deteriorating water supply could support. They get some new music from Vinyl Scratch's apartment and Littlepip cooks Party-Time Mint-Als. Littlepip enters a memory orb showing Vinyl Scratch's view of Pinkie Pie's last party. Pinkie was a Party-Time Mint-Al addict, and Twilight Sparkle confronted her about it, saying that if she didn't get help their friendship was over.
Littlepip wakes up the next morning and overhears SteelHooves laying a persuasive case to Calamity that she and Velvet are agents arranging local politics for some powerful employer. SteelHooves declares he's joining the group on their trip. DJ Pon-3 gives the news on the radio, saying that Chief Grim Star of Tenpony Tower is trying to wipe out a group of ghouls who tried to get into the tower. Despite SteelHooves's talk with him, Calamity tells Littlepip he trusts her. Littlepip enters a memory orb in SteelHooves's shack and sees Applejack annonucing the completed Steel Ranger project from Applejack's boyfriend's eyes. The group enters the headquarters of Four Stars, a pre-war public transportation company. Four Stars prepared against government intrusion and killed Steel Rangers in the lobby.
Four Stars collaborated with zebras and destroyed Manehattan with a balefire bomb they smuggled in. Littlepip finds herself wanting a Party-Time Mint-Al not to solve a problem but just for the feeling. The group enters Tenpony Tower, an outpost of class and snootiness, and more importantly the place to contact DJ Pon-3. Montery Jack runs a cheese shop there and Littlepip calls him out on his trying to rob her. A policepony walks up and Montery Jack openly agrees that he did try to rob her and he was just trying to survive a trip gone wrong. Tenpony Tower punishes robbery with execution, so he's arrested and legal processing begins. Littlepip meets Homage, DJ Pon-3's assistant, who reveals that she is DJ Pon-3 and uses a spell to alter her voice during news broadcasts so she doesn't have to watch what she says to avoid being kicked out of Tenpony Tower. Tenpony Tower was the Ministry of Arcane Science hub in Manehattan, and Homage has its access to camera feeds from cameras halfway up cloud-piercingly high towers built across Equestria. She lacks access to Fillydelphia's tower, where Red Eye has hacked his way in.
Littlepip gives the music the group found in Stable 29 to Homage and finds Velvet checking on Tenpony Tower's addiction therapy services. Littlepip storms off and tries to figure out what Montery Jack's game is by popping a PTM, talking her way past the police, and getting to his cell. Montery Jack says he confessed because he decided that he'd keep the Wasteland from eroding everything good about him away like it had done to so many, and so he'd keep his virtue, honesty, intact no matter what. Homage loves to have new music since she has so few tracks to play all the time and asks Littlepip to get some Sweetie Bell music from the headquarters of Red Racer, a scooter company Scootaloo bought. In return, Homage can provide a flux regulator, the component that would get the Sky Bandit up and running. The group arrives at Red Racer HQ, but there's a flock of manticores in its lower stories. Littlepip pops a PTM while no one's looking. She decides they'll go up the nightclub Hoofbeats and walk across a giant metal scooter that fell off the top of Red Racer and wedged between the two buildings halfway up. The nightclub only filled the first few stories; the rest of the building was the Ministry of Morale hub in Manehattan. Littlepip stuffs her saddlebags with a locker full of Party-Time Mint-Als. They find Pinkie Pie's charred skeleton with a Twilight Sparkle statuette engraved "Be Smart" that gives Littlepip clarity when she takes it. Pinkie's terminal has a recording that Pinkie tried and failed to send to Twilight where she says she's getting help and wants to stay friends, and that she's sending Steel Rangers to stop Four Stars. They cross to Red Racer and get the music. Littlepip, thinking of Montery Jack's honesty, asks Watcher if virtues are all you need, and Watcher says that a spark is necessary for ponies to work right: friendship. Littlepip asks Homage if she's seen anyone who could be compatible with her and Homage says she's interested.
Homage says that modern Steel Rangers just want to hoard technology. She and Littlepip go on a date. Littlepip asks SteelHooves about the Steel Rangers and he says there's some disagreement among Steel Rangers as to whether their oath is to the Ministry of Wartime Technology or to its ministry mare. The group heads to the ruined Horseshoe Tower to investigate some griffins' distress signal. Calamity left en route to kill some raiders. The group fights alicorns in the tower. An alicorn falls into heavily irradiated water with SteelHooves and she regenerates her wounds from the radiation. When SteelHooves is pulled out he refuses RadAway medicine since he's a closet ghoul and also regenerates from radiation. Littlepip has some trouble with a safe and pops a PTM, trying to be coy but getting caught by Velvet. Littlepip tries the memory orb trick on another alicorn, but this alicorn laughs and says she remembers. Littlepip deduces that alicorns are telepaths. After that alicorn's dealt with, they meet the griffins stuck at the tower's top under a large alicorn shield. The alicorns were after codes to a safe in the Ministry of Image headquarters that contains the Black Book, a spellbook of necromancy. The shield falls to concentrated firepower. An incoming wing of alicorns chases the group and the griffins. Littlepip's PTM high fails to find a solution for the first time. Calamity flies in, leads the alicorns over a fireworks factory's shipping area, and blows it up.
Littlepip crashed into a metal bar that went through her hoof. She enters a memory orb as anesthetic that shows a Ministry of Morale employee monitoring phone calls hearing Apple Bloom and Sweetie Belle talking. Apple Bloom said Applejack was in an elevator accident that may have been arranged by her ministry to kill her. Sweetie Belle says Rarity's been comforting Fluttershy, who's been crying ever since Rainbow Dash called her a traitor. The memory finishes, and Littlepip learns that some ghouls tried to take over Tenpony, which is known for its anti-ghoul sentiment, by paying Blackwing, leader of the griffins the group rescued, to release a horde of zombies (ghouls who've snapped and gone feral) that live in Tenpony's maintenance tunnels. Blackwing refused the job. Blackwing, true to the griffins' mercenary spirit, tries to pay the group for their rescue with a huge gun. Littlepip refuses the gun and says they owe her group a favor instead. Watcher agrees to get Blackwing to meet Gawd if Littlepip gets him something of DJ Pon-3's: a gem that functions as a memory orb. Velvet sees a balefire phoenix, one reborn from a balefire bomb detonation. Mutant vampire bats attack it and Velvet burns them all, saving the phoenix. Littlepip plans to save Montery Jack by stunning him and carrying him out of Tenpony using a StealthBuck. After Littlepip builds a stun gun, Velvet stuns her with it and has her treated for addiction. Littlepip wakes up after Montery Jack has been executed. He was a widower and cared for two foals. Littlepip calls in the favor Blackwing owes them, having him take the orphans to Gawd's territory. Littlepip hears SteelHooves has gone to the maintenance tunnels and rushes down to find that, besides ensuring that no one could open the maintenance tunnel doors again, he murdered Chief Grim Star by feeding him to the zombies.
SteelHooves covered his murder perfectly, painting it as he and Grim Star destroying the controls on the tunnel's interior while fighting the zombies, and Grim Star dying in combat. Littlepip flushes nearly all her PTMs down a toilet but hesitates at the last tin. Homage walks in and flushes it for her. They go up to her flat and Homage cooks an exceptional meal for Littlepip, who hasn't eaten in days. They spend the night together and Littlepip agrees to get Homage access to Fillydelphia's tower's cameras and radio transmitters. Homage gives Littlepip a Pinkie Pie statuette, engraved "Awareness! It was under'E'!" Littlepip gets even more clarity and feels more alive. Homage shows Littlepip a pistol that fell from the sky and vaporizes its targets. She says the zebras think the stars are eldritch abominations that delight in watching those below destroy each other, and that maybe there's something to the legends. Littlepip explains Watcher's request and Homage gives the gem to Littlepip. Littlepip enters it and sees through Spike's eyes as Rainbow Dash models Rarity's pegasus powered armor design for the rest of the Ministry Mares. Watcher sends a sprite-bot to collect the gem but Littlepip insists that she deliver it in person. Calamity gets the Sky Bandit in the air. The phoenix Velvet saved joins them. While Velvet is in the Fluttershy orb seeing her idol for the umpteenth time, Calamity tells Littlepip what Fluttershy's war-ending project was: she had the megaspells made and gave them to both sides. Watcher directs them to Dragon Mountain. When they arrive, he walks out. He's Spike.
Spike keeps Steel Rangers out of his cave, so SteelHooves stays put while the rest come inside. Spike wanted the memory gem since it shows the last time the Ministry Mares were all together. Littlepip asks Spike why he doesn't help out in the Wasteland. Spike takes her aside by herself and shows her Gardens of Equestria, a megaspell in a Crusader Maneframe that would be powered by the Elements of Harmony and cleanse Equestria of radiation and taint, making the land fertile again. Spike's been trying to bring together a group of friends with the right virtues for two hundred years. He hasn't been outside killing raiders and such because he's been defending Gardens of Equestria from potential threats like Steel Rangers and the Enclave. They return to the group and Spike's stories of the Mane Six before the war are interrupted by Enclave soldiers who want to arrest Calamity. Spike disintegrates one and the rest leave. Velvet asks what all those towers are for. Spike says they're for the Single Pony Project, whatever that is. Calamity says the Enclave uses them to grow crops in clouds. Littlepip recommends Ditzy as Laughter and Homage as Honesty.
Fillydelphia was Equestria's industrial hub. To get there, the Sky Bandit will fly over hellhound territory. Hellhounds, tainted Diamond Dogs, go through rock as if it's water and have claws so sharp they pierce standard alicorn shields. Littlepip enters a memory orb from a power plant and sees Ministry of Wartime Technology higher-ups agreeing that it's time to arrange Applejack's retirement.
Steel Rangers meet the group in Fillydelphia's suburbs. One Steel Ranger tells SteelHooves that many Rangers would follow him in his devotion to Applejack over the Ministry. Littlepip asks SteelHooves why he joined the group. He came to assess Stable 2's threat level and stayed to be good again. Littlepip enters an orb from SteelHooves's pre-war safe-deposit box, seeing him murder Applejack's chauffeur, who was in on the elevator conspiracy. Once the memory finishes, she learns SteelHooves had declined a promotion to Elder a few years back to avert a Steel Ranger civil war.
Littlepip enters another of SteelHooves's orbs, seeing Fluttershy use a healing megaspell on a battlefield, helping both sides and saving SteelHooves's life. Rainbow Dash tells Fluttershy off since it forces them to refight the battle. Fillydelphia's Steel Ranger elder asks Littlepip to enter an orb. It shows Rarity trying to sell Applejack on a scheme to make indestructible soul jar armor. Applejack vehemently objects and Rarity backs down. The elder was using it in an argument with SteelHooves, thinking it showed Applejack not caring about troops' lives. The elder has a mission for Littlepip: destroy Red Eye's research on bypass spells, which let enchanted objects ignore a specific material, e.g. bullets and Steel Ranger armor. Littlepip plans to enter Red Eye's domain alone, disguised as a slave. SteelHooves and Calamity tell the story of Canterlot's fall: the city filled with necromantic pink cloud that made objects fuse into each other, Celestia and Luna kept a shield around the city to contain the cloud and let people evacuate the surrounding area, and they died. Littlepip attaches a transmitter to her PipBuck to call Calamity when she needs to leave. While she's after the bypass spell research, the rest of the group plans to get Homage her tower access.
Littlepip joins Red Eye's slave force. Red Eye gives a speech in person. He's a stable dweller cyberpony. Littlepip finds some guards abusing some slave bullies and she kills the guards. While fleeing through a Ministry of Morale fun farm mirror house, she sees a mirror reflecting a version of herself that's bloodied and in raider armor. She gives up her escape when a bunch of foals in one of Red Eye's "train the next generation of elites" schools pull guns on her. An alicorn floats an illusory grenade towards her that surrounds a memory orb, and Littlepip falls for her own trick. The memory orb is from Pinkie Pie, whose PTM-enhanced Pinkie Sense tells her that Littlepip is watching when she feels her hoof burning. Littlepip gets sent to the arena, where Xenith the zebra is champion.
Littlepip knocks Xenith out by telekinetically choking her. She escapes the cage by surrounding it with radioactive goo to obscure the guards' aim, telekinetically picking the lock on top of the cage, and levitating herself out. She brings Xenith and her transmitter is shot. Littlepip kills an alicorn who's filled with power from radiation. Red Eye and Littlepip have a chat. Red Eye wants Littlepip to kill the Goddess, who telepathically controls the alicorns. He plans to ascend to godhood and control the sun, moon, and weather. Once he's a god he wants Littlepip to benevolently rule his empire. If Littlepip doesn't kill the Goddess, he says he'll kill her friends in the tower. The rest of the group in the Single Pony Project tower contact Red Eye. They've set up Homage's access, defeated his capturing force, and captured his right-hand griffin for bargaining. Red Eye was talking about Tenpony Tower, though. He has the balefire bomb from New Appleloosa and isn't afraid to use it.
Xenith joins the group. DJ Pon-3 warns the group that there's trouble close to home. The group visits Fillydelphia Steel Rangers headquarters again, formerly Stable-Tec headquarters. Littlepip enters a memory orb showing the Princesses approving Stable designer Apple Bloom's design for Luna's magic academy. SteelHooves and Xenith tell what happened at the academy: some zebra refugees tried to get care in the school, didn't respond to questions since they didn't know the language, and were almost exterminated when the matron panicked and briefly activated defenses. One zebra with a stealth cloak and a pink cloud bomb killed everyone in the school. After the massacre, Princess Celestia abdicated and the war really got serious, partly since most in the Zebra Empire thought Princess Luna was Nightmare Moon. The group heads to Stable 2 on Homage's warning and finds Steel Rangers invading the Stable.
The invading Rangers are slaughtering the Stable's inhabitants. SteelHooves uses the Stable's PA system to ask them to rebel and stop the atrocity. Some do rebel but the other Rangers seal them off in part of the Stable. The loyalists almost win but Gawd's griffins come to the rescue, hidden by invisibility cloaks. Records show Applejack made it into the Stable, had a foal, and died of old age. SteelHooves leaves to command the rebel Rangers.
Littlepip gets a Rainbow Dash statuette engraved "Be Awesome!" from a shack where Scootaloo stayed after the war. On taking it she feels better, nimbler, more graceful--overall, cooler. They go to Tenpony Tower, now surrounded by Red Eye troops, where a secret society descended from the Ministry of Arcane Science reveals itself to Littlepip. They run the place behind the scenes and have a megaspell chamber that needs direct sunlight on itself and a target area to bombard the target area with as many and as intense sunlight laser beams as they want. It can't be used since the sky is always overcast. The heroes travel to the Goddess's headquarters, a Ministry of Arcane Science research facility in hellhound territory. They learn that Twilight Sparkle wanted to build an army of alicorns to win the war, so she worked with her ministry to make a potion to transform ponies into alicorns. Trixie was the first test subject, but rather than taking a painstakingly measured dose, she fell into a vat when a megaspell hit the building. Afterwards she started forcing the potion into other ponies and assimilating them, starting with Twilight Sparkle. Littlepip realizes that Red Eye wants to use the alicorn potion to become a god. The Goddess wants Littlepip to get her the Black Book. Xenith, being a zebra, is immune to her telepathy.
Littlepip scans a map of the research facility into her PipBuck. Calamity observes that the taint-filled valley might act as a massive telepathic amplifier for the Goddess. Hellhounds ambush the alicorns by wonder-gluing magical energy mines to the underside of the landing pad. Velvet anesthetizes a painfully dying alicorn. She uses a disintegration ward spell on the team, which saves Calamity when a hellhound shoots a hole through his wing. The group heads to a hellhound town with a pre-war hospital so they can get medical supplies and fly away. Tainted plants dump spores on Littlepip, transferring taint to her. The Enclave had visited the hellhound town, and they built a failed sonic remote control for hellhounds.
While bagging a pile of loot in the hospital, Littlepip notices a PTM tin was in that pile, and moves on without discarding it. They find the supplies they were after and heal Calamity's wing. Hospital records reveal that taint is the alicorn potion, administered at wrong doses or to the wrong species. The group visits Gawd for some reason. In Tenpony Tower, Littlepip wakes up from another addiction treatment after she used a PTM to convince Red Eye to do something. Her memory is full of holes in recent times. She had them removed into memory orbs by Tenpony doctor Life Bloom so the Goddess can't read her mind and see how she plans to kill her when she returns with the Black Book.
Tenpony's secret society takes Littlepip's memory orbs so they can evaluate her. Most of Red Eye's troops leave from around Tenpony Tower.
A dying Steel Ranger elder tries to upload his brain into Stable 29's Crusader Maneframe. Littlepip stops him by using the override codes Scootaloo gave a top Stable pony in case the maneframe went crazy. (That pony was one of the first to die.)
The elder is put in stasis for use in a prisoner exchange with Manehattan Steel Rangers. SteelHooves rejoins the group for the occasion and to help them survive Canterlot while retrieving the Black Book. There's another danger besides pink cloud: the city's transmitters broadcast a lethal necromantic signal. Another rebel Ranger takes command for the time being. The group finds hospitality in a friendly Manehattan community, Arbu. The Steel Rangers try to kill the group instead of negotiating with them, and the group kills their powered armor troops. When Littlepip learns they're keeping two water talismans for themselves, the group tries to negotiate for them, but a fight breaks out and the other Rangers are slaughtered save two. Littlepip finds pony meat being processed in Arbu and immolates everyone in the settlement who has a mark showing they've eaten from their first kill. DJ Pon-3 reports that Littlepip may be evil.
The group leaves with Arbu's children and those who refused cannibalism. They deliver them to Friendship City, but the city's guards won't let Littlepip approach. DJ Pon-3 gets more information and sets the record straight.
The group comes to Glyphmark, a zebra town where slavers took all the adults. Since then foals have been banishing each new foal to get the zebra cutie mark equivalent. Alicorns have kidnapped some of the foals and taken them to Zebratown, a pre-war ghetto. Zebratown is right below Canterlot, and is contaminated with pink cloud. The pink cloud cuts off the Goddess's signal and the alicorns are hostile. Littlepip learns that zebras launched the megaspells because they believed ponies would kill them all if they won. The alicorns kidnapped the zebras to study their telepathic immunity. Nearly all the captives live to be rescued. The group fixes Glyphmark's drug lab (so they'll have something to trade) and repairs military robots lying around the town to act as guards. Xenith stays to teach the foals survival skills.
The rest of the group goes into Canterlot, aiming for the Ministry of Image HQ on Ministry Walk. Alicorns infest the area, so the group makes dashes from building to building. Littlepip finds a Fluttershy statuette in the Ministry of Peace HQ engraved, "Be Pleasant." It had fallen from a rotted purse on Rarity's skeleton. On picking it up she feels a surge of magic like the others, but with a greater surge from their all being together. Littlepip spends too long in pink cloud-saturated water and her PipBuck fuses with her leg. She finds a recharging StealthBuck in the Ministry of Arcane Science HQ. They get the Black Book from the Ministry of Image HQ as planned. Littlepip goes into the castle and triggers a spell to turn the dragon who guards the Royal Treasury, who has eaten the gems composing the pink cloud producing megaspell, into a mouse. She finds Princess Luna's skeleton and a complete Ministry Mares statuette collection, meets back up with the group in the Ministry of Awesome HQ, and gives the second statuette set to Velvet. A shield around the headquarter's control center has a genetics-checking bypass spell for the Cutie Mark Crusaders, and admits Velvet since she's Sweetie Belle's direct descendant. Inside is a box of memory orbs marked with a burning hoof--the sign that Littlepip is watching. Littlepip watches the orbs. SteelHooves murdered Zecora since he thought she was a zebra agent, but she was actually a double agent working for Equestria. Rarity died saving Fluttershy by teleporting her to the Everfree. Pinkie Pie walked into her office right after her last party and saw herself in a mirror from Rarity that showed the true nature of a soul. Pinkie and Littlepip had/have a chat. Pinkie decided to get help, insisted that the world's bleakness will end in sunshine and rainbows "as long as you're able to face the fire", and decided to shut down the Ministry of Morale as soon as she saved Manehattan. She had the mirror sent to a fun farm. The Single Pony Project, designed by Stable-Tec, was built to control the weather and change the seasons under one pony's control, letting pegasi focus on the war effort. Rarity was distraught by how her friends were drifting apart. To keep them together, she had her soul torn to pieces, put all but one fragment into statuettes, used a "true mirror of the soul" spell to make each fragment that wasn't hers take on the nature of the appropriate friend's, and sent a complete set to each of her friends and Princess Luna, besides keeping one for herself. The group leaves Canterlot by going over a waterfall and lands in Zebratown.
Velvet encounters raiders and kills them. The group goes to the outskirts of hellhound territory. Red Eye's troops are there, now dead, killed by alicorns. Littlepip goes alone to the Goddess and stalls her. An alarm comes up on her PipBuck: "Run. Balefire bomb detonation in 43 minutes." Littlepip comprehends her own plan: She took an invisibility cloak from Gawd's griffins, used PTMs to convince Red Eye to use his balefire bomb on the Goddess, and had Xenith plant the balefire bomb while cloaked. Littlepip leaves the Black Book to its doom. Grand Pegasus Enclave diplomats arrive, offering the Goddess an alliance. After taking evasive maneuvers through a pool of alicorn potion, Littlepip goes into a bomb shelter designed to withstand a megaspell. One large explosion later, the Enclave hijack the radio waves, declaring that they are coming to save Equestria.
Littlepip wakes up to find that she lost a leg when the shelter internally collapsed and regrew it in the radiation since she's so tainted she's become a partial alicorn. Twilight Sparkle, possessing an alicorn, saves Littlepip. Littlepip plays Pinkie's message to her. Twilight Sparkle fades away. Ditzy, powered up on radiation from the recent detonation, brings Littlepip back to her friends. A hellhound kills SteelHooves. The rebel Rangers, now calling themselves Applejack's Rangers as SteelHooves wished, hold a funeral. The group sees the Enclave destroy Canterlot in the distance. Velvet learns that Fluttershy gave megaspells to the zebras. This, along with her raider encounter, convinces her that people are, whether intentionally or not, on the whole bad. She refuses to accompany the group saving people since she thinks people aren't worth saving. Littlepip, Calamity, and Ditzy meet an old Dashite who shows them a recording from the Ministry of Awesome HQ: Rainbow Dash bringing the memory orbs for Littlepip after the war and rigging the place to set off alarms in every Ministry of Awesome hub if anyone went in there again so that if Littlepip arrived she'd know. That means that the Enclave thought surfacers were after Ministry of Awesome technology, specifically the Single Pony Project, their only source of food. They then tried to set the Goddess against Red Eye, who they blamed for the intrusion, but when Littlepip killed their diplomats (including a High Council member) it was war. The group gets captured by the Enclave and they swap cutie mark stories. Littlepip got hers when she found a lost colt. Calamity's youngest brother frees them. The Enclave, who aim to end Red Eye's empire, attack New Appleloosa in retribution for their giving him the balefire bomb. The group arrives in time to intervene. Ditzy flies up, distracting the attackers, then flies down at extreme speed.
Still irradiated up, Ditzy pulls off a sonic radboom, crashing the attacking Enclave aircraft and peeling away the clouds for miles around. Enclave troops come in to depopulate the village, but get called away to reseal the clouds. Homage broadcasts a call to resistance from a Single Pony Project tower she hijacked. Enclave troops arrive to kill her, but only find a recording playing and a bomb made from a star blaster battery. They're vaporized. Watcher tells Littlepip that the Wonderbolts, the Enclave's premier assassins, are after her for using the balefire bomb--and they have her PipBuck tag ID from a terminal she clumsily hacked, so they know where she is at all times.
Gawd's twin kids join the group to help them fight the Enclave. Velvet's back, having decided that only helping people who deserve it isn't the point of helping people. Littlepip realizes that Velvet is Kindness and Calamity is Loyalty. Calamity plans to use Life Bloom's memory magic to show his story to the Wonderbolts, hoping that they'll join him once they find the truth. The group gets the Enclave's invasion schedule from their temporary comm post at the top of a skyscraper. Gawd's son dies in the process. The group heads to the Everfree Forest, hoping the environment will nullify the Wonderbolts' flight advantage.
The Wonderbolts finally get out of committee and come to kill Littlepip. Fluttershy is an Everfree tree, transformed by killing joke, a more malicious and mobile strain of poison joke. Velvet takes a wounded hellhound in as a patient.
Littlepip lets drop that she asked Watcher to gather some particular people in his cave. An Enclave aircraft en route to Red Eye's Everfree base gets taken down by something the Enclave calls "the demon" broadcasting the Canterlot lethal necromantic signal. The group uses a couple of Gawd's invisibility cloaks and Littlepip's recharging invisibility device to hitch a ride on the Enclave air battleship spearheading the attack. They go down into Red Eye's base, where Littlepip gets seperated from the group and meets Red Eye. He has the alicorn potion ready and asks her to join him in becoming a god to save the world from itself and guide people into goodness. Also present is Calamity's brother Autumn Leaf, an Enclave general, who Red Eye also invites to join him as a god. Littlepip says that people don't need guidance to be good and refuses the offer. Hellhounds enter, controlled by perfected Enclave sonic remotes, and Red Eye is killed in the mayhem. Littlepip shoots Autumn Leaf dead, and meets Velvet, who used the base's resources to give the hellhound a cybernetic replacement leg. The group sees an aircraft full of bombs and pink cloud ram the battleship, sending it crashing to the ground.
Littlepip tells her friends she wants to control the Single Pony Project and roll away the cloud layer, bringing back the sun and forcing the pegasi down to the surface Then the Enclave's lies would be clear and most pegasi would start helping their fellow ponies, rather than trying to kill everyone they think might take what little they have of the Single Pony Project (and thus agriculture) away from them. Her friends object to the part of this plan where she goes behind an incredibly strong force field, enters a coma-like state, and is separated from everyone who loves her, but they agree that it has to be done. Alicorns come to Velvet since she relieved an alicorn's pain once and ask her to help them by making male alicorns so their species can survive. She agrees to do it eventually. Lionheart, a Canterlot ghoul who was in Luna's guard, joins the group. He's the "demon" who's been fighting the Enclave along with his buddy, the pink cloud-breathing formerly draconic mouse. The group goes to the nearest Applejack's Rangers base and brings some rangers to Watcher. Lots of old friends are there, including Ditzy and Gawd. Gawd plans to build New Canterlot and bring Equestria under the rule of a republic once the war is over. Velvet wants to bring education and healthcare to the Wasteland via alicorns. Littlepip tells everyone the plan: some, including the Applejack's Rangers, will guard Gardens of Equestria, some, including Spike, will make a surgical strike at the Single Pony Project, and some will arrange for Tenpony Tower to use their megaspell on the armies approaching Fillydelphia, preventing the Enclave from destroying Red Eye's industrial progress. Littlepip realizes that her cutie mark relates to PipBucks' tag feature, not her proficiency with computers. Her special talent is finding the right people. Gawd's griffins clear the clouds over part of Manehattan. Ditzy soaks up radiation from Fillydelphia's centuries-old ground zero and radbooms over the city, clearing the clouds. The megaspell is cast and sunlight lasers destroy both sides' more devastating equipment, leaving them just with infantry. The force field around the Single Pony Project, which even the Enclave can't penetrate, was set to only allow Rainbow Dash and the Princesses passage. Littlepip thinks that since she's mostly alicorn and has a perfect image of Dash's soul, she can get through. She can't. Remembering Pinkie's requirement of facing the fire, Littlepip calls Spike over and asks him to burn her. He refuses. Littlepip reveals Twilight Sparkle's fate to him. He disintegrates her. She dies.
Littlepip realizes that her virtue is sacrifice. The mirror reflecting her soul showed the moment she was willing to give herself up for the caravan while fighting "raider" Calamity. She's rematerialized inside the Single Pony Project building. As she suspected, she's been sent to Princess Celestia through Spike's teleportation magic. Celestia fled Canterlot once Luna died and, knowing that she was dying, uploaded her mind and poured her soul into the Single Pony Project's Crusader Maneframe. Rainbow Dash had the maneframe disconnected from weather control since she hated the mind-in-a-computer stuff, so Celestia could only watch the Wasteland through the tower cameras. Littlepip sends a message to Spike telling him what's happened by the magic Celestia always used to send Spike letters, cast through the maneframe's spell matrix. Littlepip uses the mind uploading scanner to record her memories of her story for distribution through the Wasteland so people can know what side to join. Those memories comprise the story's prologue and chapters.
Littlepip has taken control of the Single Pony Project. Velvet and friends aim to save Fluttershy with a modified poison joke cure, then gather all the prospective Bearers and activate Gardens of Equestria.
Ten years later, Fluttershy finishes reading the story (with some discretion on which parts to glaze over) to some foals in the New Canterlot Republic. Equestria is graced with green grass and blue skies. An alicorn foal shows off a shield spell to her. Radiation is imported to power engines and heal ghouls. Velvet married Calamity, and Ditzy and Lionheart are together. Littlepip sometimes hosts guests, contrary to her earlier fears of isolation. Arbu is now a prison. Fluttershy prepares to use her unspecified authority, perhaps presidency, to arrange for a hellhound sanctuary's creation.