On her 14th birthday, Anna Akechi, a second-year junior high student from the town of Makoto Mirai, encounters a fairy named Pochitan, who suddenly sends her back from 2027 to the same town nearly three decades earlier. Stranded in 1999, Anna crosses paths with Mikuru Kobayashi, a girl her age who dreams of becoming a renowned detective.
Almost immediately, a bride becomes the victim of a mysterious theft when her tiara vanishes. Refusing to stand by, Anna and Mikuru awaken the ability to transform into magical girls known as Pretty Cure, taking it upon themselves to uncover the truth behind the incident. Their investigation leads them to an elusive group calling themselves the Phantom Thieves, whom they confront as the group continues their thievery.
As further incidents loom, Anna and Mikuru resolve to stand against the Phantom Thieves and prevent future crimes. They soon learn that the stolen items contain Makoto Jewels—sources of power the Phantom Thieves seek for their own ends. However, that same power is also vital to Pochitan, who needs it to return Anna to her original time. Hoping to prevent this power from falling into the wrong hands, the two press forward, balancing their duty to protect others with Anna's desire to find her way home.
