Chapter 643 is titled "Phantom".
While the Neptune army is fighting the New Fish-Man Pirates, Robin frees the slaves. Then she gets captured by Hammond with a net, but still defeats him by making two clones. Zeo crawls to Brook, but Brook hears him and stops his sneak attack. He explains his powers and then attacks Zeo again. Usopp dodges Daruma's charge and tells him why he cannot lose. The Ammo Knights from the Air Tank contact Neptune and he grants them the use of the national Den Den Mushi. With that they tell the people that Noah is on a collision course with Fish-Man Island and they are to evacuate. Then there is a lot of static during a short conversation between Luffy, Shirahoshi, and the knights. Fukaboshi reveals what Hody Jones is, that he is a monster created from a grudge of the fish-man race against the humans.
Gyoncorde Plaza is a site of carnage and chaos now that the royal guards have joined the battle. Robin is doing as Jinbe asked of her and is freeing the slaves. Hammond manages to capture her in one of his Trawl Nets. He pulls the net back, but Robin creates a replica of her torso on Hammond's back. Robin then appears at his feet, and the two Robins begin contorting Hammond's body until they break his back. The ex-slaves begin fighting against the fish-men who enslaved them.
The scene changes to Brook, who realizes he has lost track of Zeo. Zeo is on the ground, slithering toward Brook. However, Zeo says loudly the name of his technique, allowing Brook to hear his voice, and the skeleton immediately thrusts his sword in the direction the voice came from, stabbing Zeo just below the neck. Zeo plays it off as a technique to destroy weapons, in order to damage the tip of Brook's sword, but even Brook does not believe him and knows he got stabbed. Zeo throws his chain and catches Brook around the neck, taking his head off. As his head falls, he remembers tapping into the true powers of the Yomi Yomi no Mi during his training. He learned of a powerful energy that allows his soul to stay in this world, despite having died once already, and how he has gained control of his very soul.
While Zeo is celebrating his victory, Brook remembers that it is the power of soul that is keeping him alive, and reattaches his head to his body while thinking this, stunning Zeo. Brook tells him that his attacks will not harm bone. He then takes out his sword, saying it was sharpened by the Longarm Tribe, calling it Soul Solid, saying its slashes bring forth the cold of the frigid underworld.
Usopp is telling Daruma not to do something. Daruma tells Usopp he will leave his friends as scraps on the sea floor. He then somehow lights himself on fire and flies at Usopp using a technique called "Hi-Daruma Cutter". Usopp shoots at Daruma but misses. Daruma mocks him for being weak and only being able to shoot dud shots. Usopp simply tells him he is finishing his traps and that Daruma will be taken down in three moves. Daruma says he is lying, and Usopp admits that he used to lie a lot, but adds that he cannot do that anymore, as he now has it within himself to back up his claims.
As the battle rages on, the Minister of the Left receives a call on a baby Den Den Mushi from the border defense. The border defense informs the minister that Noah is once again on a collision course for the island. The Minister of the Left tells the person to tell the whole island, using the nationwide broadcast. They make the announcement and people start fleeing. Nami is shocked to see Noah coming back, and Jinbe wonders if Shirahoshi and Luffy are safe. The man from the Air Tank then talks to Luffy, and their conversation is picked up on other channels. Bits of a conversation between Luffy and Shirahoshi are heard. All over the island, people are surprised at what they are hearing. Luffy is attempting to do something to stop Noah. Then Fukaboshi's voice is heard through broadcast system. He tells Luffy what Hody Jones really is.
The scene changes to outside the island, where Fukaboshi tells Luffy, as well as the rest of the island, that Hody is a monster born from circumstance. The New Fish-Man Pirates are a group that thrive on hatred and resentment. They hate in order to forget the pain of those who came before them. They also hate that the anger toward humans may one day fade away. Fukaboshi asks the people to trust the pirates for the sake of the island's safety. There is then a flashback to when Fukaboshi asked Hody what happened to him to make him hate humans so much. The answer that Hody had only been seen mouthing earlier was a single word, "nothing". Hody goes on to say that the fish-men were chosen by heaven to hand down judgment on humanity. The chapter ends with Fukaboshi saying that the New Fish-Man Pirates' hatred lacks personal experience and will. They are just empty beings with no substance what so ever.
- Mont Blanc Cricket, Masira, and Shoujou are seen for the first time after the timeskip. They still have the Hercules beetle that Luffy gave them before the Straw Hats set off to Skypiea.
- Robin's cloning abilities are now named and further demonstrated. She also uses a new variation of Clutch called Double Clutch.
- Brook reveals what he learned over the timeskip about the mechanics of how his Devil Fruit keeps him alive. He demonstrates that this allows him to reattach his head to his body as well as envelop his sword in the energy of his soul, making it very cold. He also reveals that his sword was sharpened by the Longarm Tribe and named Soul Solid.
- Usopp has set traps to snipe Daruma in three moves.
- The slaves freed by Robin join the battle against the New Fish-Man Pirates.
- The entire Fish-Man Island population is told to evacuate because Noah is on a collision course with it.
- Octopako is once again seen as a background character in this chapter.
- Fukaboshi reveals to the whole island why Hody hates humans, and its not being an ex-slave like Tiger, or mistreatment and losing Tiger like Arlong, but purely his violent upbringing and propaganda that led to his hatred.
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