The story revolves around five humans: Jake, Marco, Cassie, Rachel and Tobias, and one alien, Aximili-Esgarrouth-Isthill (nicknamed Ax), who obtain the ability to transform into any animal they touch. Naming themselves "Animorphs" (a portmanteau of "animal morphers"),[6] they use their ability to battle a secret alien infiltration of Earth by a parasitic race of aliens resembling large slugs called Yeerks, that can take any living creatures as a host by entering and merging with their brain through the ear canal. The Animorphs fight as a guerilla force against the Yeerks who are led by Visser Three.

Throughout the series, the Animorphs carefully protect their identities; the Yeerks assume that the Animorphs are a strike force sent by the Andalites, the alien race to which Ax belongs that created the transformation technology, to prevent them from conquering Earth. To protect their families from Yeerk reprisals, the Animorphs maintain this façade.

Though the Animorphs can assume the form of any animal they touch to acquire the DNA, there are several limitations to the ability. The most vital is that they cannot stay in animal form for more than two hours, or they will be unable to return to human form and the morphs become permanent. Others include having to de-morph back to human in between morphs, only tight clothing being able to be carried over with a morph, and having to consistently maintain concentration during a morph to prevent the animal's natural instincts from overwhelming the human intellect. A benefit to morphing is that it allows the team to heal any superficial, non-genetic injury, sustained as a human or in a morph. Also, while in morph, they can telepathically communicate with anyone nearby.