Led by Yamato, Naruto Uzumaki, Sakura Haruno, and Sai are assigned to capture Mukade, a rogue ninja who is pursuing the ancient chakra Ryuumyaku located underneath the Rouran ruins. While the Ryuumyaku has been sealed by the Fourth Hokage, the group fails to prevent Mukade from releasing its power. Consequently, a strong energy burst engulfs both Naruto and Yamato before they can escape.

As he awakens in a magnificent yet hostile kingdom, Naruto meets its young queen Saara and three Konohagakure ninjas on a top-secret mission. They reveal to him that he has time-traveled to Rouran 20 years into the past! To make matters worse, Mukade has already infiltrated the royal court, becoming the naive queen's most trusted minister under the alias Anrokuzan.

Joining forces with the three ninjas, Naruto must protect Saara's life without fail to stop the villain's plans and return to the present.

Naruto: Shippuuden Movie 4 - The Lost Tower is set approximately in between episodes 152-156 of the Naruto: Shippuuden anime series at the beginning of the "Pain's Assault" arc.

Along with the film, an exclusive animated short feature named Naruto Soyokazeden Movie: Naruto to Mashin to Mitsu no Onegai Dattebayo!! was shown as well. To celebrate the movie's release on July 31, 2010, a one-hour episode titled "Naruto Shippuuden Big Adventure! The Quest for the Fourth Hokage's Legacy" was broadcasted on July 29, 2010. The DVD version was issued on April 27, 2011. The film was released in North America on September 17, 2013 by Viz Media.

According to a Pia Corporation survey, Naruto: Shippuuden Movie 4 - The Lost Tower had been well received not only by children but also by women in their teens and 20s. The movie has an animanga adaptation as well, released exclusively in Japan on August 4, 2011.