Dr. Vegapunk is the smartest character in One Piece, but prior to the Egghead Island arc, readers had only seen Vegapunk being mentioned in conversations. Oda had been tantalizing the fanbase for over a thousand chapters, and finally, in the first arc of what has been dubbed the "final saga", the genius scientist made his first-ever appearance.
In the early chapters of the Egghead Island arc, Oda introduced the fans to Vegapunk's different satellites, which was rather confusing as none of them seemed to match the expectations of the fans, who believed that the scientist was old and weary. Once again, Oda made the readers wait, and eventually, in One Piece Chapter 1066, the real Vegapunk made his debut.
The Will To Survive
In the subsequent chapter, Vegapunk told Luffy that it was fate that brought him to the island. The scientist sought Luffy's help to get off the island, but he has yet to provide an answer. Back i​​n chapter 1062, it was teased that Vegapunk wants something from the Straw Hats. Shaka, one of Vegapunk's satellites, openly expressed his desire to meet the Straw Hats and asked Lilith to escort them to his location.
Ever since coming into contact with them, he has been providing them with valuable information about the past, including the massacre of Ohara and the ancient kingdom. This is an indicator that Oda is building up toward something big. Away from Egghead Island, Rob Lucci's group was given the job of eliminating all the bodies of Vegapunk for an unspecified reason. Given the fact that CP0 is a secretive organization, it would be nigh impossible to get ahold of any information about their plans for normal people.
However, Vegapunk is the furthest thing from ordinary. Shaka was seen talking to Dragon and telling him that his death is imminent, which shows that he is already aware of the intentions of the World Government. The sudden decision to kill Vegapunk is certainly perplexing and leads one to wonder, "Why does the World Government want to eliminate Vegapunk, who has served them for many years?"
Ally Of The Worst Criminal In The World
By now, it has been firmly established that Vegapunk is close friends with Monkey D. Dragon. The two of them were together at Ohara after the massacre, and from their conversation, it became evident that they go way back. The dialogue between the two characters revealed several big details. One of the big confirmations was that Dragon invited Vegapunk to join the Freedom Fighters, but he refused as he would not have enough funding to make new inventions. Interestingly, when Dragon said that he was furious with the actions of the World Government, Vegapunk reminded him not to lose sight of the goal, which implies that the two of them were mutually working on a goal.
If the World Government has somehow figured out the connection between the two, it would explain why they want to get rid of him. However, the odds of Vegapunk being found out are low; after all, it would be unbelievable to see the smartest man in the entire world make a mistake. The other possibility is that the World Government believes that Vegapunk has served his purpose. Vegapunk's biggest job after the time skip was to perfect the Pacifista to replace the Shichibukai so that the Navy would not have to rely on pirates.
With the Seraphim project complete, they do not need Vegapunk anymore. Also, it would be foolish to rule out the possibility of the World Government feeling threatened by Vegapunk; after all, he can create things that no other person can, and he has even designed Egghead Island after the ancient kingdom that existed centuries ago. This could have made the higher-ups in the World Government anxious, so they want to erase him before he can cause any significant damage.
Possible Betrayal?
Vegapunk has created six satellites that help him to get work done quicker. Each satellite has a part of Vegapunk's personality. The six satellites are as follows: Shaka (The Good), Lilith (The Evil), Edison (The Thinker), Pythagoras (The Wise), Atlas (The Violent), and York (The Greedy.)
A prominent theory that has surfaced is that Lilith might actually be a mole, and she could be leaking Vegapunk's secrets to the World Government. However, this theory is flawed considering all the satellites have to go to Punk Records every day to synchronize what they have memorized. So, if Lilith were to try to betray her creator, then she would have to circumvent this particular issue, which doesn't seem likely at all.
Will The Straw Hats Help Vegapunk?
Vegapunk's plea for help has not been answered yet by Luffy, but it would be unlike him to reject it. Before Luffy reaches a decision, he would definitely want Vegapunk to help Jewelry Bonney and Kuma. So, in the upcoming chapters, fans can expect the truth behind Kuma's transformation to be revealed.
The assassins from CP0 have already arrived at Egghead Island, and they are waiting for permission to dock. Shaka has made it clear that he won't be allowing CP0 to dock, and this decision is certainly not going to go down well with Lucci. Under normal circumstances, CP0 would have no problem eliminating Vegapunk and his satellites, but the presence of the Straw Hat Pirates changes everything, although Lucci and co. have no idea that they have company. It is very likely that things will escalate rapidly in the next chapter, and it could even result in a conflagration. Sadly, One Piece manga is on a break, so there will be no chapter this week and fans will have to wait a bit longer to read what happens next.