Like Kamen Rider × Kamen Rider W & Decade: Movie War 2010, Movie War Core is split into three parts. The Kamen Rider W portion of the film is titled Kamen Rider Skull: Message for Double. The story, taking place after the series epilogue, features Akiko Narumi preparing for her wedding before considering canceling it when the Futo Kamen Riders are distracted by the Pteranodon Yummy who has somehow acquired the Memory Memory. The Pteranodon Yummy uses these powers to reveal to Akiko how her father and Shotaro's mentor, Sokichi Narumi, became Kamen Rider Skull with Shroud's aid
The Kamen Rider OOO portion of the film is titled Kamen Rider OOO: Nobunaga's Desire . The Kougami Foundation has discovered the mummified remains of Oda Nobunaga and have created a Cell Medal-based homonculus of the man with his memories. Dubbed Nobunaga, he runs from the Kougami Foundation and into Eiji Hino's care. However, Nobunaga attempts to resume his conquest of Japan while targeting the descendants of those responsible for his down fall. But when forced into becoming a mindless Greeed, Eiji must stop Nobunaga before it is too late.
In the final portion of the film entitled Movie War Core is convergence of the two films that brings the casts and characters of W and OOO to fight the evil energy-based giant Kamen Rider Core.