The story is set in Shahalta, a tiny European city-state floating in the air with practically no contact with the outside world for years. The government is transitioning from a monarchy to a republic, and to celebrate the occasion, a national treasure exhibition is being held. Lupin infiltrates the exhibition for the secret royal treasures, but not before sky pirates snatch them first.

(Source: ANN)

On the ocean floor, Lupin is once again seeking a treasure hoping to get on Fujiko's good side. As Zenigata chases them on sea and land, people around the gang begin to vanish mysteriously. The fog rolls in and Mamo Kyosuke appears in a burst of light; he claims to be from the future and seeks revenge on Lupin III for what Lupin XIII has done to him. Mamo hurls Lupin, Jigen, Goemon, and Zenigata 500 years into the past; as two warring factions fight over a legendary shrine dedicated to time travel, Lupin must find a way to survive the past to ensure his future.

(Source: Lupin III Encyclopedia)

This movie is a remake of episode 13 in the original Lupin III series.

Half a year after the battle in Okinawa, Excel was looking for a new Mototsumitama to revenge on Reishin. Excel met Mikami and decided to contract with her. Before making the contract, Excel looked back at the encounter with Steiner.

Shortly before the upcoming festival, a year after the end of episode 12, Daigo decides to find a girlfriend to dance with in the festival. Will he be able to do so?