The Marines fail again to catch the Straw Hats. After escaping from the Marines, Nico Robin (Ms. All Sunday) appears from inside of the Straw Hats ship. She manages to persuade the crew to let her join. Pell is seen at the end standing over his own grave.
It's the day for Vivi's speech and her decision whether or not to continue to be with the Straw Hats. Meanwhile, Bon Clay and his crew attempt to protect the Straw Hats from Hina.
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.
Now that the battle has ended, the outcome is tallied. Igaram appears with proof of Cobra's innocence, as well as Kohza 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 defeats Crocodile by punching him through solid bedrock. When Crocodile falls, the rain-drops calm the soldiers.
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 fights with Crocodile by using blood on his fists. Meanwhile Vivi finds the bomb, and calls the Straw Hats together.
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 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.
As Kohza 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.
When Vivi reveals Crocodile's plan to Kohza, he attempts to stop the fighting, but is shot. Crocodile reveals that he has set up a massive bomb in the city.
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 can't cut. As Zoro nears death, he must discover the secret to "the breath of all things".
While Crocodile reveals to Vivi about the ancient weapon Pluton, Nami attempts to defeat Miss Doublefinger with her most powerful attack: The Tornado Tempo.
Nami faces off against Miss Doublefinger and tries to figure out her new weapon, the Klima Takt (Climate Baton), at the same time.
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.
Albeit severely beaten and bruised, Usopp and Chopper have finally defeated the Mr.4 team. However, Mr. 2 has figured out Sanji's weakness.
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.
Vivi's attempts to stop the rebel army go to waste, and she is attacked by Mr. 2 Bon Clay, but manages to escape. Meanwhile, the battle of Usopp and Chopper vs. the Mr. 4 team begins.
The revolution is on the verge of starting and the crew comes out with a plan that could stop it.
Luffy is left for dead by Crocodile, but is helped by the mysterious Miss All-Sunday. The rest of the Straw Hats reach Alubarna.
After escaping from Rain Dinners, the Straw Hats and Vivi cross the desert to Alubarne, where the final battle will take place. Crocodile, however, manages to catch Luffy, beginning the first round of their battle.
Chopper distracts Crocodile while Sanji frees the rest of the crew, but find themselves trapped yet again. Smoker's view on Luffy changes a little.
Most of the Straw Hats are helplessly trapped, but Crocodile is contacted by "Mr. Prince".
Baroque Works' plan to take over Alabasta is set in motion. The king is kidnapped and framed for a crime, and the rebel army begins to move.
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.
The crew travels to the city of Rainbase to take down Sir Crocodile and Baroque Works, but run afoul of Smoker and Tashigi.
Vivi and Luffy disagree in how to stop the rebel army and Baroque Works, leading to a fight.
Baroque Works plan starts to take effect, and for that, the Number Agents gather to meet Mr. 0. Meanwhile, crew finds out that the Rebel Army has moved out of Yuba and headed to Katorea, and the rebel leader Khoza is determined to attack.
Zoro, Chopper and Luffy manage to get themselves lost and stumble across some huge underground ruins.
Ace finds out that Blackbeard isn't in Alabasta after all, and leaves the group to continue looking for him. He leaves Luffy a mysterious piece of paper, explaining that it will let them meet again.
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.
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.
Nami and Vivi found themselves an easier way to travel in the desert and leave all men behind. While trying to catch up with them, Ace gets lost. Luffy and the rest of the gang find the Desert Pirates, and Vivi meets a figure from her past.
After leaving Erumalu, the Straw Hats plus Vivi & Ace continue through the desert, facing the many dangers of it.
Ace decides to travel with the Straw Hats, as he is hunting for a man known as Blackbeard. The group arrives first at the 'Green City' of Erumalu only to find it abandoned to the desert. Vivi and Nami explain what Dance Powder is and what it has done to Alabasta.
Ace fights Smoker while the Straw Hats run for their ship. Luffy reunites with his brother, and together take down agents of Baroque Works.