Wired (MLP / Original Summary)

The story takes place in a distant-future Ponyville, now a bustling city with an expansive underground market. Very few characters actually overlap with canon, and the setting itself is heavily modified for the scifi / cyberpunk genre.

Entropy Enterprises marketed Wiring as a replacement for natural abilities, to improve them or to allow different species of pony to use the same magic. Wiring also allows essentially a telepathy network and linking to some machines, and it eventually worked up to the princesses themselves being Wired (the story opens on a flashback, though not specified as one, to Luna and Celestia's wiring booting up for the first time)

After Celestia and Luna are wired, most of the population follows suit (though many already had it) and once they have enough control, Entropy imprisons Celestia and Luna to use them as a power source; the actual sun and moon are destroyed during this process. With this power, Entropy overthrows the Crystal Empire as the crystal ponies naturally resist the Wiring process. Entropy uses the wiring to wipe everyone's memory of that period, so people believe Celestia and Luna are still ruling from Canterlot. False memories are implanted of public appearances and known correspondences with the rulers.

The story follows:

• Crescent: a Changeling gang leader who keeps a firm hold on the future-Ponyville criminal underground. Classic 'powerful criminal with a heart of gold'. Modded her own Wiring, and the Wiring of the Changelings in her pod, so she's not on the 'official' network and can't be affected by Entropy Enterprises. She knows the Princesses have been absent, but it's a topic so irrelevant to her life that she's never realized the average pony still believes they exist.
• Spiderwick: an older teen Earth Pony who grew up in the aforementioned criminal underground, who is currently living low and taking care of a younger foal who was orphaned. He's also Wired and off the grid, but to a much lesser extent and against his will. He's linked on a local network run by a pony he only knows as Warden, who keeps track of him and a handful of other errand runners. Through his work, he knows Crescent, though he only knows her as her public name, Eclipse. She calls him by his public name, Redback, but she knows more than she lets on.
• Anastasia: chose her own name; a blind Pegasus whose parents were employed by Entropy. Her father is killed when he tries to smuggle information out of the company, and Ana leaves home and accidentally finds herself becoming fast friends with Cinnamon.
• Lone Wolf and Nox: Earth Pony and Kirin treasure hunters, known only as a pair. They're currently exploring the tundra for the Crystal Empire, because its crystal and thats so much money. They're boyfriends, and bastards, and neither of them are Wired; Kirins with Wiring tend to report chronic physical discomfort with the devices, potentially due to their more sensitive hearing, and Lone hasn't gotten any because he thinks it's a waste of money.
  
• Cinnamon: a Pegasus who is also Wired with a unicorn implant so she can work with more detailed machines. Lone and Nox know her as an inventor, and Anastasia knows her as an explorer with a handmade VR rig that allows her to control machines to travel alongside Lone and Nox. Lone and Nox also believe Cinnamon is an alicorn, and hiding her true identity - Ana is blind, and exclaimed in confusion when she heard magic, and Cinnamon turned off her mic before she explained the situation.
  

Lone and Nox, accompanied by Cinnamon-in-a-robot, fall through the ice of the tundra into the Crystal Kingdom and find the aptly named Crystal, who is (though not revealed in the story before I stopped writing) the Crystal Heart, enchanted to take a pony form so she could protect herself and her power when Entropy Enterprises stormed the kingdom. Lone and Nox bring her back to neo-Ponyville with them after discovering that Entropy was behind the Kingdom falling and not - as they'd learned from other ponies, and the publicly accessible histories - the third rise of King Sombra. The reason for overthrowing the kingdom and destroying it instead of simply threatening it into keeping its distance is because the Crystal Pony's hearts were used as conduits for magical power, and in turn powered Cinnamon's robots.

Cinnamon gets them to bring Crystal to her house, as she's the only one of the three who lives in Ponyville, and when they do so she kidnaps her because - surprise! - Cinnamon has been the owner of Entropy Enterprises the whole time, and her machines that accompany Lone and Nox are being tested for military use in extreme circumstances. Lone and Nox dont have the clearance to break in to the company, but Ana does since her parents are still on the record, and she breaks in to try and get Crystal out. Lone and Nox, investigating Cinnamon's workshop, see the mech she's repairing and make the connection that the Crystal Ponies were killed to power the military robots.

While all of this is happening, Crescent, Spiderwick, and their associated characters are dealing with the fallout from Entropy setting off huge bombs under the city and collapsing most of it. Crescent is angry-grieving, because this is Her City and Her Family and dear god someone is going to pay for this. On their side, they're learning more about what Entropy/Cinnamon has planned, and figure it out practically as it's happening.

Entropy also wiped the memory of Discord from the populace; Cinnamon drains Crystal's energy to give her enough power to control chaos magic, and then drains him of his, turning her into what is, essentially, a god. Ana breaks in, realizes what's happening, goes 'what the hell?', and flees deeper into the building; she ends up finding Luna and Celestia, and they - their magic heavily drained - voluntarily give her their remaining power so she can fight back. While those two duke it out, Entropy is taking control of the ponies on the official Wired network and turning them against the others, intending to stifle the fighting so it can be handled. The ponies who aren't on the official network are Not Going To Let That Happen, so they're all fighting as well.

Cinnamon and Ana continue to duke it out at explosive proportions; Ana's power is draining faster, since she's Wired and Entropy is still siphoning off of the Princess's magic through her. Surprise two though, which Cinnamon reveals to her during the fight, her parents aren't even actually her parents. Ana's not even a real pony. She's a robot - and she's Cinnamon's design. Cinnamon gloats about that, expecting Ana to give up, but Ana just kicks the shit out of her anyway because she's seen what Entropy Enterprises did and she refuses to be a part of that (and it's only the Princess's energy keeping her from being forced to fight on Entropy's side.)

Their fight continues while the city ponies successfully subdue most of the on-grid ponies and make a move on the Entropy building itself; Cinnamon sees them and uses it as a hostage situation - Ana gives in and Entropy can do what it wants, or Cinnamon will just release the energy she still has and blow the whole city off the map.

Ana does not give in, but uses her power to neutralize Cinnamon's explosion. In doing so, she is also destroyed; the ending of the battle for everyone else is a very anticlimactic fizzle of sparks and magic a few hundred feet in the air.

The main cast is like, oh shit, Ana / Crystal / Cinnamon, and rush up to the roof to try and see if there's anything left. There is very plain evidence that both ponies are dead, and equally plain evidence that Ana was a robot, to which they all kind of go 'holy shit'. They release the Princesses, Discord and Crystal and, lacking a better plan, get to rebuilding the destroyed parts of town and tending to the survivors. Crescent spends a lot of her time reWiring ponies so they're no longer linked to Enterprises and/or whatever company decides it's a good idea to broadcast a similar signal.

Crystal is having a Hard Time dealing with the fact she kind of had a hand in Ana dying, so she spends a lot of time in secret learning how Cinnamon's machines worked and how to rebuild one; she does eventually build a much more simplified model and salvages Ana's memories from the destroyed body, so Ana gets her happy ending rebuilding the city and helping to remove or de-grid the wiring of the ponies living there (which she is very good at as a robot with her capabilities unlocked). Lone and Nox adopt Spiderwick and the kid spiderwick semi-adopted, Pumpernickel; Crescent's crime network cleans itself up (though it doesn't need it much) and takes the place of Entropy as a service and goods provider until the city can go back to the way it was before Entropy.