After their triumphant success over Harrow's End, Harmony's Elements celebrate their victory. But as time goes on, they realize the infection has escaped the city, all due to a group of ties to Harrow who want revenge. As they venture back into the heart of the unknown, they encounter old friends, new enemies, and discover of secrets buried under the ruins as they delve back into the nightmare they had once thought they had stopped...

(If you have not read the previous story, you can find it here.)
Mission I: http://www.fimfiction.net/story/21572/resident-ponevil-operation-equestrian-downfall