"Soreike! Anpanman: Baikinman vs Baikinman!?" is a feature-length anime film based on the popular children's series "Soreike! Anpanman." The story revolves around the iconic hero Anpanman, a superhero made of anpan (a sweet bread filled with red bean paste), who protects the world from evil forces. The central conflict arises when Baikinman, a recurring antagonist made of germs, creates a clone of himself named Baikinman X. This clone is designed to be stronger and more cunning, posing a significant threat to Anpanman and his friends.

The narrative begins with Baikinman X betraying his creator, Baikinman, and asserting his dominance as the superior version. This internal conflict between the two Baikinmen escalates, leading to chaos in the world. Baikinman X's enhanced abilities and ruthless nature make him a formidable adversary, forcing Anpanman to confront a more dangerous enemy than ever before. The story explores themes of identity, rivalry, and the consequences of unchecked ambition.

Anpanman, alongside his loyal friends such as Shokupanman (a bread superhero) and Currypanman (a curry-filled bread hero), must devise a strategy to defeat Baikinman X while also dealing with the original Baikinman's schemes. The film incorporates moments of teamwork, courage, and the importance of friendship, which are central to the "Anpanman" franchise. The climax involves a high-stakes battle where Anpanman and his allies must use their unique abilities and ingenuity to restore peace.

The film maintains the series' signature blend of lighthearted humor, action, and moral lessons, making it accessible to its young audience. It also introduces new dynamics to the established characters, particularly through the rivalry between Baikinman and his clone, adding depth to the conflict. The resolution emphasizes the enduring values of kindness and perseverance, reinforcing the core messages of the "Anpanman" series.