Long after Twilight and her friends leaving Ponyville and returning to Canterlot, Ponyville started to grow. It turned from a small little town to one of the biggest cities in Equestria.
One regular night in Ponyville, a mare was walking through the empty and darkened streets. As she's walking, she notices something strange about the manhole ahead of her. She felt like avoiding getting close to that manhole.
She shrugs it off and continues walking. As soon as she passes through the manhole, a creature raises the lid and pulls her inside. She tries to scream for help, but nopony heard or noticed her or the monster.
C.P.U.D
George had just moved into Ponyville, he works as an photographer and he used to be famous fashion photographer in Fillydelphia, but later he lost all his fame due to his inactivity and he moved to Ponyville to start new photographing projects and even possibly become big and famous again.
Currently he's working on an article about homeless ponies that live underground in Ponyville and their difficult living conditions. The ponies that have resorted into living underground are very jumpy and generally not that nice.
Meanwhile in the Ponyville police station, captain Bosch got an report of an old mare that tried to steal an weapon from a cop. Bosch gives her one phonecall, so she calls George and tells him that she's in jail. Being her friend, George bails her out.
When they are outside, George asks her:
"What do you need a weapon for?"
"It's not for me, it's for Victor, my son." She responds.
"Why does Victor need a weapon?"
"He's crazy, he thinks he saw a monster and he injured his hoofs."
They decide to go see Victor so they start heading for the nearest subway station. It just so happens that he lives... Underground.
They go in a subway station and climb ladders up and down.
"Why can't you just live in a cardboard box like every other bum?" George asks jokingly
She laughs and they finally get to her and Victor's place.
As soon as they walk in, Victor asks her if she got a weapon for him. She says that she only got bandages and Victor cries that he doesn't need bandages, he needs a weapon.
"What do you need a weapon for Victor?" George asks.
"Kill them."
"Kill who?"
"Ugly fuckers!" Victor yells
"What ugly fuckers?" George asks Victor.
"He's sick, can't you tell!?" She yells and starts to remove a old and bloody bandage from Victor's back hoofs. That's when George sees a huge bite taken out from Victor's hoofs.
Later Bosch get's a phone call from a pony named A.J "Reverend" about a huge group of missing Undergrounders that come up every day for soup in his Soup Kitchen.
Bosch arrives at A.J's kitchen and as soon as he steps in, he notices that he is not welcome and get's alot of weird looks from all the homeless ponies. Like always, A.J is there serving soup to them for free.
"Well well, A.J Reverend. What's all this missing ponies stuff about?" Bosch says to A.J
"Calm down Lieutenant..." A.J says but is interrupted by Bosch.
"It's Captain."
"Okay okay, fine. Do you wanna hear this or what?"
"So, who's missing?" Bosch asks A.J.
"My family." A.J responds.
"Your family?"
"My regulars, my ponies here."
Bosch and A.J sit down on a empty table.
"I have been looking all over for them and i can't find them!"
"Where do you think they would be?" Bosch asks him.
"Some of them are street ponies, they are probably out on the street but most of them are undergrounders. Look, in my cellar i have a hole broken through the wall that connects to an old sewer system, that's where they live, ten or twelve of my regulars. Those are the ponies that disappeared!"
"All of them?"
"Yes."
"How long has it been?"
"It's been, about two weeks now and i still can't find them."
"Two weeks? You haven't seen ANY of these ponies for TWO WEEKS?" Bosch asks with a surprised look on his face.
"Yeah, expect for one. Val."
Bosch and A.J go see Val, and try talking to them, but Val doesn't respond. After many tries at communicating with him, Bosch tries to move closer to him.
"Be careful, he has been pretty jumpy lately." A.J tells Bosch as he approaches Val.
As soon as Bosch gets close to Val, he pulls out an knife and tries to slash Bosch with a razor sharp knife. Bosch jumps back and dodges the attack. Val doesn't attack again, he was just trying to defend himself.
"Woah, where did he get a knife like that?" Bosch asks after backing up from Val.
"All undergrounders are looking for weapons now, the regular inspection of the sewers just started and everypony's getting all jumpy again and dusting off their old shotguns."
Bosch decided that he can't help about the missing ponies if the undergrounders are this unfriendly and just left.
Next day he noticed that her wife had gone missing a few nights ago so he contacted A.J again and decided to help him with the missing ponies problem.
"What is it now, didn't you just say that you couldn't help?" A.J asks slightly annoyed.
"Your call isn't the only one we got."
"Aha, i knew it. What is it, who's missing? Did Celestia go missing or your mom? Answer me Bosch!"
"My wife, okay. I think she was walking home from a meeting, and she was never seen again."
"Hey Bosch, i went to see the sewers shortly after you left, you won't believe all the stuff i found." A.J says to Bosch and they go underground through the hole in A.J's cellar.
After walking a while in the sewers, A.J and Bosch come across alot of stuff, and then they stumble upon some property of the nuclear powerplants.
"Look at this thing, they wear these things in nuclear powerplants to detect radiation! I called the nuclear powerplants and i told them that i had to return some of their stolen property. They sure were nervous and nopony could come up with any ideas how it got there."
That's when Bosch and A.J notice an Geiger counter. Bosch picks it up and turns it on. It first doesn't detect anything, but after a short while it goes to the maximum radiation level and slowly lowers down to zero again. That's when they hear a blood chilling scream echoing in the sewers.