When Cloudsdale's water supply is contaminated by industrial runoff, chlorine seems like the natural choice for disinfection. Celestia sends four cars of it to the area, shipping via the Equestrian Railway. Now, chlorine is highly toxic, and, in nature, takes the form of a gas. And when the line breaks down at the one station between the two cities, you have a recipe for disaster.
Meanwhile, Twilight Sparkle is preparing for a busy day of experiments. She's ready to log everything in her daily journal. But the sound of screeching metal interrupts her work, and she and all her friends head out to see the commotion.
Five months later, a decon team from Canterlot discovers Twilight's journal. Adding it to other documents they've recovered, they may be able to piece together just what happened during the Ponyville Quarantine.
"I've found from past experiences that the tighter you plan, the more likely you are to run into something unpredictable."
-MacGyver
This story will be told in the form of various documents (mainly Twilight's journal).