The film's story is set in the Doll Kingdom where dolls reside. Happiness Charge PreCure are asked to help by a women named Tsumugi when the sudden appearance of Saiarks begin wrecking havoc upon the Kingdom. However all is not what it seems with the mysterious man Black Fang dwelling in the shadows.

The mysterious, delicious world of CooKingdom, which rules over all the cuisine in this world. CooKingdom has closely guarded the Recipe-Bon, in which it's written how to prepare any dish. But, oh no! One day, it gets stolen by the Bundoru Gang! The Bundoru Gang plans to monopolize everything for themselves, and their next target is the Cuisine Fairy Recipeppi... The Energy Fairies have come to Oishi-Na Town in the human world in search of the Recipe-Bon. With their help, an unexpected turn of events leads to three ordinary girls transforming into Pretty Cures! They stand up to the Bundoru Gang, to recover the Recipe-Bon, and to protect everyone's delicious smiles!

Earth has been conquered by the evil Illumidus Empire, with parallels drawn to the U.S. post World War II occupation of Japan. Captain Harlock with a group that will become his life long friends begin their fight against this tyranny visited upon the planet Earth, with no regard to the costs the struggle will have on them, caring only for the ideal of restoring freedom to the people of Earth.

After successfully holding off the invasion by Aftokrator, the Border Defense Agency prepares an away mission into the Neighbor's dimension. However, like in previous scouting expeditions, only A-rank teams are certain to secure a spot. As the B-rank wars continue, Osamu Mikumo and the rest of Tamakoma-2 quickly fight to the top in an attempt to obtain a promotion before the operation begins. Meanwhile, a new Neighbor ship approaches Border Headquarters. Noticing that the attackers are targeting the Border Expedition Ship, forces are hastily sent to combat them. However, with fewer squads available due to the proceeding rank wars, the organization is sent into disarray. This latest offensive from the Neighbors shrouds the fate of the all-important expedition ship in uncertainty.