In Mouseheart, Hopper is just an ordinary pet shop mouse before he escapes and finds himself deep within the Brooklyn transit tunnels, and in Atlantia, a glorious utopian rat civilization. Soon, Hopper is caught in the crosshairs of an epic battle, one that crosses generations and species. As the clashes rage, Hopper learns terrible, extraordinary secrets: Deadly secrets about Atlantia. Painful secrets about his friends. And one powerful secret about his destiny.

In Hopper's Destiny, the tunnels are in a state of chaos, Queen Felina and her growing army of feral cats is a greater threat than ever before. When exterminators raid the tunnels, Hopper is snatched away and taken back up to the daylight world. Upland, Hopper makes new allies, and as he enjoys the sights and sounds of Brooklyn, he wonders if he will ever make it back into the tunnels to restore safety and prosperity, as foretold by La Rocha's prophecy.

In Return of the Forgotten, the subway tunnels are still dangerous to all rodents. Hopper is determined to reach out to Pup, his brother-gone-bad. But then the youngest of Zucker and Firren's new litter goes missing, and all signs point to Pup as culprit. Meanwhile, Firren is guarding a shameful secret from her past. A secret that may hold damaging consequences for not only Firren, but all of Atlantia.