More thoughts and a basic 'script' for My Little Warhammer 40000.
Straight NMM and C were both killed, C was kept alive by unicorn magic.
Unicorns would be psykers in this case. Magic would require such energy that most unicorns couldn't stand a day, which is the 'testing' for the talented ones. Naturally, our protagonist is a talented one.
After C has died, gryphons, buffalo, even zebra, as well as monsters from the EFF and evil ponies have started attacking the principality of Equestria. Princes (Blueblood's line) rule, with the help of a court of advisors. Even females of the line are called princes, Princess being reserved for Celestia. At the time of the story, Blueblood is in command.
Six advisors. One of the Administratum, Assassinorum, Navis Nobilite, Tech priests, Munitorum, Equisition.
The Equisition.
Equisitor Venator
Unicorn. Usually hides his horn. Is a unicorn detector. Finds our protagonist. Only character at start.
Equilyte Fluttershy
Pegasus. First one to welcome protagonist to the Equisitor's team. Harder than usual, but still mostly Fluttershy.
Equisitor Sparkle.
Equistor of team. Unicorn. More concentrating on battle powers than tricks.
Draconopath Spike
A bit crazier than usual. Repelled by Rarity.
Applejack - arbite, perfectionist against corruption, clashes with Rarity.
Rarity - culexus, not completely slobby but knows what she can get away with
Pinkie Pie- DEATH cultist.
Rainbow Dash- Guardsman.
Discord is leader of evil.
Protagonist: Markon.
Opening scene: Arbites and guardsponies are combing the city, looking for a pair of fugitives. Unicorns hidden for years, they are presenting great problems for the guards. They've killed arbites. Not obvious good guys. We finish the scene with a civilian pony finding the baby Markon on their doorstep.
Scene change.
The high lords of Equestria are meeting. We discover that the two fugitives have been captured and sent to Celestia. They discuss the problem of having the child of such powerful psykers still at large. Equisition representative informs them that the child will be found, and his best Venator is on the hunt, while laughing at the pun. Is established several years have passed.
Scene change.
Venator finds Markon. Sends him to Celestia.
Scene change.
Markon relates the tale of his survival in Celestia's chamber to his stablemates at Blueblood's Scholum. Characters aren't given much importance, but is established they are at the end of their studies, and it is a graduation day tradition. They graduate and are assigned duties. Fluttershy collects Markon. Is still fairly timid, but never uses hesitators or stumbles over her words. Stares down one of the other graduates who hits on her.
Scene change
Markon meets Sparkle. "You're late. I hope that isn't a habit.". Rainbow Dash and Applejack meet him. They're quite disciplined. They don't make a good impression on Markon. Rarity does, but she still scares him. Pinkie Pie just broods in the corner and ignores him. This should be her usual behaviour outside of combat. Spike comes in late, having had to send a message to command. He clicks with Markon, being the only other male. Spike has a reply from command, with orders from High Command: retrieve six relics of the Lunar Heresy, rumoured to be weapons of Celestia herself. Prophecy says they are the only weapons capable of defeating a reborn Luna, which prophecy again says is about to happen. Unknown to all the ponies, neither Celestia or Luna are dead: they are instead banished to their respectful celestial objects. Further unknown is that the relics are the only chance for Celestia to be reborn. They are, however, CORRUPTED!
A clue is revealed as to their last known location. An ancient cache of relics was lost to Chaos several hundred years ago.
Scene change.
Nightmare cultists prepare for her rebirth. Once she is reborn, revolts occur across the entire country. The High Lords hold Canterlot, and many of the rebellions are crushed. An Equisition fortress is taken. Massive casualties on all sides. Buffalo, Zebra and EFFF use the confusion to make massive gains of territory. Guardsponies fight a losing battle. Equisition forces prepare for an assassination mission to take out NMM.
Scene change
Sparkle and the rest of her group make their way to the fortress. Several conflicts are fought between cultists and Sparkle. Spike receives a message telling them of the situation at large. They hurry to the fortress. Once they get there, they discover the elements of Harmony. They retrieve them and hurry out.
Scene change
Back at the capitol. The rebels are attacking Canterlot itself. Guardsponies are keeping them back, but they are bringing up siege equipment. The other cities are holding fast, mostly, but the concentrated effort on Canterlot is the real reason for it. Equisition forces have concentrated Unicorn attacks on different leaders, and assassins have spread fear in the enemy ranks, but nothing seems to be enough.
The Custodes are called out. Their mission? To retrieve Sparkle and her group. With the EoH.
Scene change
Sparkle and her group come within sight of the capitol. They can see the host of NMM. The catapults are raining down rocks on the walls. Custodes ponies fly above, out of range of hostile magic. They get Sparkle and team into the city. As they get to Equisition High Command, the walls are broken and the enemy surges into the city. Street to street fighting begins, and the Celestian ponies are the ones at a disadvantage to begin with. They are forced back slowly but surely. All the while, the Equisition is trying to purify the relics.
NMM's forces are beginning to slow down now. In a last ditch attempt, she decides to lower her anti-magic barriers, trying to lure the Equestrians into a trap and be finished with this battle.. The relics by this time are purified. The custodes and Sparkle's team are sent in, along with all the other Equisition ponies able to fight. Teleporting their way in, they are surrounded.
The Custodes surround the Equisition and cover them. Spears and shields provide a wall to prevent the enemy forces getting in. The Equisition attempts to activate the EoH, and each, one by one, fails to activate. They are surrounded, trapped, and cut down to a pony. NMM wins.