After being summoned to Canterlot castle, Clockwork is told of the new Rainbow Factory located in Cloudsdale. With his experience working with Starswirl the Bearded on eliminating the previous Rainbow Factory, Clockwork is now the only pony for the job.

As Clockwork and his acquired partner, Lucktwist soon find out, the new Rainbow Factory is just the begining of a series of terrible happenings across Equestria. The more problems they come across and attempt to fix, the worse the rest of the world gets.

Discovery is made of a Discord Virus that leaked from the future, but the past isn't immune to the futuristic disease and Equestria takes a massive turn for the worse. Will Clockwork and Lucktwist be able to save Equestria or will the duo realize that you can't protect Equestria from itself?