The film opens with Nefeltari Vivi flying with Pell in a brief flashback. Returning to the present, Vivi and the Straw Hats meet Crocodile’s subordinate Mr. 2 Bon Clay. Mr. 2 shows the Straw Hats his devil fruit ability, which allows him to assume the form and voice of anyone whose face he has touched. Vivi describes a brief history on how the Baroque Works leader Crocodile has used Dance Powder while posing as the country’s hero. He has also tricked the rebel and royal armies into fighting each other. Once in Alabasta and after crossing the desert, the Straw Hats find the rebel’s base deserted, while the rebel army, led by Vivi’s childhood friend Koza, witnesses the port town Nanohana being burned by members of Baroque Works disguised as soldiers of the royal army. The rebels decide to attack Alubarna, where at the same time Mr. 2 impersonates the king, Nefeltari Cobra, and orders the royal army to engage. Meanwhile in the desert, the Straw Hats are intercepted by Crocodile and his partner, Ms. All Sunday. Crocodile aims for Vivi, but Luffy stays behind and distracts him, while the other Straw Hats escape. In the ensuing fight, Crocodile defeats Luffy by impaling him through the chest with his hook and buried alive.
The Straw Hats arrive at Alabasta’s capital city, Alubarna, where the officer agents of Baroque Works are already waiting for them. The Straw Hats lure them into the city, allowing Vivi to try and stop the approaching rebels. Vivi’s attempt fails and she rushes to the palace. Meanwhile, Usopp and Chopper defeat the officer agents Mr. 4 and Miss Merry Christmas, while Sanji manages to defeat Mr. 2. Vivi finally reaches the palace and convinces the acting royal army captain, Chaka, to blow up the palace to make the fighting sides listen to her. However, Crocodile and Ms. All Sunday arrive and interfere with her plan. Back in the streets, Nami defeats Ms. Doublefinger and Zoro learns to cut steel by defeating the blade-bodied Mr. 1. Back at the palace, Koza witnesses Crocodile questioning Vivi’s father who stands nailed to the wall, about the ancient weapon Pluton. He and Chaka attack Crocodile, but are quickly defeated. With the two armies’ leaders in his control, Crocodile engulfs the palace plaza in a sandstorm, making it even harder to stop the fighting. After that, he follows his partner and the king into the royal mausoleum. Luffy arrives and follows Crocodile. In the streets, Vivi and the remaining Straw Hats try to find a bomb set by Baroque Works to wipe out both armies. Luffy and Crocodile fight in the mausoleum. Crocodile hits Luffy with his poisonous hook, but Luffy is not stopped. The Straw Hats find the bomb, as well as Mr. 7 and Miss Father’s Day in the city’s clock tower. Vivi takes out the agents and prevents the bomb from being fired; however, Vivi discovers that the bomb has a timer. Pell arrives and supposedly sacrifices himself to save Alabasta. Meanwhile in the mausoleum, an enraged Luffy breaks Crocodile’s poisonous hook and defeats him.
Back at the plaza, it starts to rain and, with Chaka and Koza presenting the defeated Crocodile as the rebellion’s orchestrator, the fighting stops. It rains for three days. After that, Luffy wakes up and a banquet is given for the pirates. News arrives that a marine fleet is on their way to Alabasta. The Straw Hats decide to leave as fast as possible, leaving Vivi with a choice. The next day, she appears at the coast, to say farewell to the crew. From there, she uses a transponder snail to broadcast a speech through the country. The film ends with Vivi asking whether she was still their friend, but the Straw Hats show the sign of their friendship on their arms. In the end credits, Vivi finds Pell alive and peace eventually returns to Alabasta.