Three years have past since Twilight Sparkle's ascension, and things could not go any smoother. At least it WAS going great until a deadly virus suddenly is killing off everypony.

Twilight and the gang are told by Princess Celestia herself to not get involved, yet that seems a bit ominous, so they decide to work under the radar. In order to finish the job however, they need somepony's help. They hire an expert, Doctor Whooves.

With the Doctor's help, the Main Six must figure out not only how to stop this virus, but also the culprit who started this monstrosity.

Despite all their precautions, that doesn't mean that they all will escape it unscathed...