The Straw Hats, with Kureha's assistant Tony Tony Chopper, finally arrive at Arabasta, which is on the verge of civil war. Vivi must reach the rebels and tell them the real cause behind the conflict, but Crocodile, leader of Baroque Works and one of the Seven Warlords of the Sea, will not just stand by and watch. In the end, Baroque Works, marine forces, pirates, the royal guards, and the rebel army clash in a battle that will determine the fate of the country itself.
Crocodile appears to stop rampaging pirates. Luffy and his crew meet Mr. 2 Bon Clay who shows off his devil fruit power and Vivi sees a shocking sight.
Luffy separates from the rest of the crew, right after arriving at Alabasta's port city of Nanohana. The crew dons disguises while Luffy learns of Dance Powder.
While in Nanohana, the Straw Hats encounter Smoker and Tashigi. A powerful pirate named Portgas D. Ace appears.
Ace fights Smoker while the Straw Hats run for their ship. Luffy reunites with his brother, who has joined the Whitebeard Pirates after leaving home, and is searching for a former crewmate named Blackbeard who killed a fellow member.
Ace decides to travel with the Straw Hats, as he is hunting for a man known as Blackbeard.
After leaving Erumalu, the Straw Hats plus Vivi & Ace continue through the desert, facing the many dangers of it.
Nami and Vivi found themselves an easier way to travel in the desert and leave all men behind.
After hearing that a small village has fake Rebel Army bodyguards that have been keeping peace, Vivi asks the men of the crew to test if they're worthy of staying.
Still trekking through the Alabasta desert, the crew beats up a giant desert scorpion for lunch, while Vivi tells Nami about her past and her friendship with Kohza.
Ace fights against a bounty hunter, who claims to have defeated Blackbeard, although this was a lie to lure Ace out and challenge him in order to inspire his children to follow their dreams.
Zoro, Chopper and Luffy manage to get themselves lost and stumble across some huge underground ruins.
Baroque Works plan starts to take effect, and for that, the Number Agents gather to meet Mr. 0. Meanwhile, the crew finds out that the Rebel Army has moved out of Yuba and headed to Katorea, and the rebel leader Kohza is determined to attack.
In Yuba, Luffy learns that Toto was entrusted by Cobra to watch over the land and figures out a way to stop the sandstorm.
After the struggle, Vivi decides to go after Crocodile with the Straw Hats. The crew travels to the city of Rainbase, but run afoul of Smoker and Tashigi.
Most of the Straw Hats, along with Smoker, are trapped by Crocodile. Vivi reunites with the royal guardian Pell, but is captured by Miss All-Sunday. Crocodile reveals his invincible Devil Fruit power.
Baroque Works' plan to take over Alabasta is set in motion.
Most of the Straw Hats are helplessly trapped as Vivi tries desperately to get the key to their cage. but fails. Crocodile is contacted by someone known as "Mr. Prince."
The identity of "Mr. Prince" is revealed.
After escaping from Rain Dinners, the Straw Hats and Vivi cross the desert to Alubarne, where the final battle will take place.
Luffy is left for dead by Crocodile, but is helped by the mysteríous Miss All-Sunday. The rest of the Straw Hats reach Alubarna.
The revolution is on the verge of starting and the crew comes out with a plan that could stop it.
Vivi tries to call out to the Rebel Army, but fails because of a Baroque Works infiltrator in the Royal Army interferes.
Things look hopeless for Usopp & Chopper as they continue to suffer from every attack that the Mr.4 team makes. However, the tides may be beginning to turn as Usopp learns what it truly means to be a man.
Albeit severely beaten and bruised, Usopp and Chopper have finally defeated the Mr.4 team. However, Mr. 2 has figured out Sanji's weakness.
Though Mr. 2 discovers Sanji's weakness, Sanji still defeats his opponent after an evenly-matched fight. Meanwhile, before Vivi could give the word to blow up the palace, Crocodile appears.
Nami faces off against Miss Doublefinger and tries to figure out her new weapon that Usopp made, the Clima-Tact.
While Crocodile reveals to Vivi about the ancient weapon Pluton, Nami attempts to defeat Miss Doublefinger with her most powerful attack: The Tornado Tempo.
While Miss. Doublefinger's fight with Nami was challenging, Zoro is having an even more difficult time fighting Mr.1: A man who can change his entire body into steel - something that Zoro cannot cut. As Zoro nears death, he must discover the secret to "the breath of all things".
When Vivi reveals Crocodile's plan to Koza, he attempts to stop the fighting, but is shot. Crocodile reveals that he has set up a massive bomb in the city.
As Koza tries to stop the Rebel Army, both sides are once more fighting due to the intervention of Baroque Works. Vivi is thrown to her certain death when Luffy saves her and challenges Crocodile to a second round.
Luffy fights Crocodile with more success this time by using water, but still loses this round. Meanwhile, the other Straw Hats hurry to locate the bomb before it goes off. Nico Robin forces the king to take her to the tomb where the Pluton Poneglyph is hidden.
Crocodile joins Robin in the tomb, and orders her to translate the Poneglyph. Robin tells him that Pluton was not mentioned and that it was only about history, but Crocodile figures out that she was lying and stabs her in response. When Luffy recovers from the last round of fighting, he chases after Crocodile into the tomb.
Luffy fights with Crocodile by using blood on his fists. Meanwhile Vivi finds the bomb, and calls the Straw Hats together.
Vivi finds the bomb inside of the clock tower, but the Mr. 7 pair of Baroque Works are there to protect it. Vivi defeats them, but she realizes the bomb cannot be stopped so easily. It has a timer, and right before it blows up, Pell shows up and takes it into the atmosphere, where he sacrifices himself to save Alabasta.
Luffy defeats Crocodile by punching him through solid bedrock. When Crocodile falls, the rain-drops calm the soldiers.
Now that the battle has ended, the outcome is tallied. Igaram appears with proof of Cobra's innocence, as well as Koza telling everything. Tashigi and Smoker both are rewarded for taking on Crocodile, but neither one of them believes that is right, considering the Straw Hat pirates did all the work.
Luffy is rescued from the collapsed tomb where he fought Crocodile and brought into Cobra's palace to rest. When he awakens, a magnificent banquet is thrown for the pirates, then, the Straw Hats are invited to enjoy the hot spring steam room inside the palace.
It's the day for Vivi's speech and her decision whether or not to continue to be with the Straw Hats. Meanwhile, Bon Kurei and his crew attempt to protect the Straw Hats from Hina.
The Marines fail again to catch the Straw Hats. After escaping from Marines, Nico Robin (Ms. All Sunday) appears from inside of Straw Hats ship. She manages to persuade the crew to let her join. Pell is seen at the end standing over his own grave.
