"Entropy dictates that everything, eventually and inevitably, will come to an end. The Wastelands ended. Not entirely, quite yet, but the days of scavenging, fighting for survival... Those are gone now. But it's threatening to come back..."

In the centuries that followed Sunshine, the Wasteland was slowly pushed back as civilization steadily re-established itself.
But the Wasteland returns with a new enemy for Equestria. The sudden appearance of the Drowned, horrifying bipedal zombified creatures that slowly tore down and retook some twenty percent of established lands, sparked an Equestrian Civil War between the two leading factions of modern Equestria, the Jackal Republic and the Twilight High Council.
In the wake of the destruction the War had caused, former T.H.C. operative Rover is re-acquired by his employers and sent on a journey to determine who the real foe is- the Jackals, or the Drowned- and to ultimately delay the impending second apocalypse.

Read Fallout: Equestra: http://www.equestriadaily.com/2011/04/story-fallout-equestria.html
Note: FoE: The Drowned is a crossover fanfiction. Important elements from: The Drowning(iOS game), Fallout: Equestria, and MLP:FiM.
Unless referenced, no other Fallout: Equestria side story applies to FoE: The Drowned(i.e. Blackjack might not exist here, unless stated otherwise).