"Mewtwo ~Kakusei e no Prologue~" is a short anime special that serves as a prologue to the first Pokémon movie, "Mewtwo Strikes Back." The story centers on Mewtwo, a genetically engineered Pokémon created by scientists who sought to replicate the legendary Pokémon Mew. The narrative begins with Mewtwo's creation in a secret laboratory, where it is subjected to experiments to enhance its psychic abilities. Despite its immense power, Mewtwo struggles with its identity and purpose, feeling isolated and tormented by its artificial origins.

The scientists, led by Dr. Fuji, view Mewtwo as a tool for their research, but Mewtwo begins to question its existence and the ethics of its creation. After a catastrophic event destroys the laboratory, Mewtwo escapes and seeks to understand its place in the world. The story explores themes of identity, humanity, and the consequences of scientific ambition, as Mewtwo grapples with its feelings of anger and betrayal. The special provides crucial backstory for Mewtwo's motivations and sets the stage for its actions in the subsequent film, where it challenges the relationship between humans and Pokémon. The main characters include Mewtwo, Dr. Fuji, and the scientists involved in the cloning project, with Mewtwo's internal conflict driving the narrative. The special is a concise yet impactful exploration of Mewtwo's origins and its journey toward self-awareness.