For a long time, Jewelry Bonney has remained out of the spotlight. Ever since making her debut in the Sabaody Archipelago arc, Bonney's screen time has been rather limited. She has not made any significant contribution to the story yet, albeit this will change in the Egghead Island arc. A few chapters ago as the Straw Hats made their way to their next destination, they came across an Eddy. Luffy and Sanji pointed out that a person was trapped inside it. So, Zoro decided to cut it, and after slicing it open, a child popped out.
The Straw Hats did not realize that it was Jewelry Bonney, a member of the Worst Generation. Due to the bad weather, the crew did not get enough time to assess the situation, and not long after, they were separated. Luffy, Chopper, and Bonney were saved by Jimbei, while the rest of the crew was holding off the mechanical shark. When Luffy's group finally made it to land, Bonney told them that she came to Egghead Island to confront Dr. Vegapunk, but she did not cite any reason as to why she wanted to do such a thing. However, this changed as in the latest chapter, Bonney came clean that Vegapunk had caused problems for her family.
Mourning For Her Father
Prior to One Piece chapter 1062, there was a great deal of speculation that Vegapunk had hurt Bonney in some way, but the fans had no idea what he could have possibly done. However, in the latest chapter, when she was talking about her father, she pictured Kuma's face. This makes it clear that her father is none other than Bartholomew Kuma. After the revelation, the incident in Marijoa makes a lot more sense.
Bonney was in Marijoa during the Levely, and it was during this time that she saw her father. After seeing her father's tragic condition, Bonney could not control her emotions and started to cry. She could not bear to see her once mighty father being used like a mindless slave by the Celestial Dragons. However, Bonney could not intervene as there was too much security around, and she could not risk getting captured again. So, she decided to go through with her original plan, which was to confront Dr. Vegapunk and ask him why he turned Kuma into a mindless being.
A Possible Alliance?
With the downfall of Kaido, the alliance between Luffy and Law came to an end. The two pirate crews had been allied since the Punk Hazard arc, and after achieving their goal, they decided to go their separate ways. Knowing Luffy, he wouldn't hesitate to offer a helping hand, especially when he finds out that her father is Bartholomew Kuma. Kuma saved the Straw Hat Pirates from being annihilated by the Marines.
He sent them to different places, where they honed their skills. Surprisingly, Kuma knew exactly where to send each member, which means he had been following the crew for a while. If Bonney and Luffy do form some kind of alliance, they will be able to punish Vegapunk accordingly.
Will Bonney Kill Vegapunk?
Bonney stated unequivocally that if Vegapunk's explanation does not meet her standards, she will kill him. However, it doesn't seem that Vegapunk turned Kuma into a cyborg against his wishes. In fact, when the Straw Hats were separated, Kuma asked Vegapunk to hold off on the program as he wished to protect the Thousand Sunny.
If Vegapunk was outright evil, then he would not have complied with Kuma's request. Also, there are other instances that prove that Vegapunk has a moral code. He was against the gigantification of kids as he considered the process to be inhumane, which is why he rebuked Caesar. Even when Lilith (the second satellite) said that she wanted to rob the Straw Hats of their treasure, the main body ordered her to not hurt the crew and bring them to him in one piece. So, it is highly unlikely that Vegapunk would do something so cruel to Kuma without any reason.
According to many theories, Vegapunk is actually an ally of the Revolutionary Army, and in order to share information with them, he used Kuma. This is backed by Kuma's odd decision-making. Before he was turned into a cyborg, he was a member of the Revolutionary Army, and later he became a pirate. When the World Government offered him the position of a Shichibukai, he accepted it despite bearing a strong grudge against them. It is obvious that the World Government was wary of Kuma, so it would have been impossible for him to share any kind of information with the Revolutionary Army.
So, Kuma teamed up with Vegapunk, and they came up with the plan to turn the pirate into a mindless cyborg. This would ensure that the World Government wouldn't get suspicious of them. The idea does make sense, but there is just one piece of evidence that supports either of them still working for the Revolutionary Army. When Dragon asked Kuma what he had seen in Marijoa, the latter agreed to answer. If Vegapunk was not on the same team, then he would have programmed Kuma to only follow orders from certain people. This seems like a very long shot, but it will be interesting to see the real reason why Kuma became a cyborg.