Throughout the events of Story Mode, each of the six characters Maypul, Forsburn, Zetterburn, Orcane, Kragg and Wrastor encounter a shadow replica of an existing character. For instance, Kragg must defeat an Abyss Clone of Maypul, and Zetterburn an Abyss Clone of Orcane.

Once every character (except for Absa and Etalus) realises that they have been fighting a common enemy, they band together in a last-ditch effort to save Aether, taking on The Gatekeepers to finally rid Aether of these shadowy monstrosities.

Each Abyss Clone shows identical movesets to their Aetherian counterpart, and their skins can be obtained by leveling their respective character to 10 in Abyss Endless mode.

On multiple occasions in Story Mode, they appear to be intelligent, with Abyss Orcane intentionally disrupting the coronation ceremony in the Fire Empire, and Abyss Wrastor trading a map of the Aetherian kingdoms' vulnerabilities with the Air Armada's commander for a valuable collection of goods from the Water Trading Company.