High schoolers Mitsuha and Taki are complete strangers living separate lives. But one night, they suddenly switch places. Mitsuha wakes up in Taki’s body, and he in hers. This bizarre occurrence continues to happen randomly, and the two must adjust their lives around each other.

In a parallel world that resembles modern Japan, alien lifeforms known as "Muttsu" (Trick) fell from the sky in 2025 and wiped out many cities. Nine years later, pilot Yuzuru Midō, and her assistant, Rin Sagami, use a mecha made out of an enemy's remains discovered in Japan. However, battle causes memory loss for the pilot, and they must unravel the mystery as to why.