Shinkalion: Change the World

Once upon a time, a mysterious enemy, Unknown, suddenly appeared. The "Super Evolutionary Railway Development Organization," commonly known as "ERDA," develops a countermeasure: the Shinkalion, a robot that transforms the Shinkansen, in preparation for the threat. Taisei Ōnari, a second-year junior high school student, goes to Shinkai Gakuen Junior High School in search of clues about his older sister, who disappeared two years ago.

Synopsis from Anime News Network