"Eiga Precure All Stars New Stage 3: Eien no Tomodachi" is a crossover film that brings together the Pretty Cure teams from various seasons, uniting them in a shared narrative. The story centers on the bond of friendship and the challenges that test it. The Pretty Cure teams face a new threat in the form of Fusion, a mysterious entity that seeks to disrupt the harmony between worlds by exploiting negative emotions. Fusion creates a distorted version of the Pretty Cure teams, known as the Dark Precure, who embody the doubts and fears of the original heroes.

The narrative begins with the Pretty Cure teams gathering for a festival celebrating their unity. However, the celebration is interrupted when Fusion begins to spread its influence, causing chaos and turning people against one another. The Dark Precure emerge, challenging the original teams to confront their own insecurities and weaknesses. As the conflict escalates, the Pretty Cure must rely on their friendships and the strength of their bonds to overcome the darkness.

Key characters include the original Pretty Cure teams, such as Cure Black and Cure White from "Futari wa Pretty Cure," Cure Bloom and Cure Egret from "Futari wa Pretty Cure Splash Star," and many others from subsequent seasons. Each team brings their unique abilities and personalities to the fight, emphasizing the theme of unity in diversity. The Dark Precure serve as dark reflections of the heroes, forcing them to confront their inner struggles and reaffirm their commitment to protecting the world and each other.

The climax of the story involves a powerful confrontation between the Pretty Cure and Fusion, with the heroes combining their strengths to create a new, unified form known as the Miracle Lights. This transformation symbolizes the power of friendship and collective effort, ultimately allowing the Pretty Cure to defeat Fusion and restore peace. The film concludes with the teams reaffirming their bonds and celebrating their victory, highlighting the enduring nature of their friendship and the importance of working together to overcome adversity.