Undoubtedly one of One Piece's most enigmatic yet significant characters is Dr. Vegapunk. The majority of the Marines' weapons, including the Seraphims and Pacifistas, were principally created by the brilliant inventor. Both good and bad things have been done using his creations. The World Government had its sights on the brilliant inventor, according to recent developments in the manga. Fans wonder why Dr. Vegapunk joined the World Government in the first place given that he also appears to have connections to the Revolutionary Army.
The Straw Hats have made discovery after discovery since arriving on the futuristic island of Egghead. The Straw Hats have had several opportunities to speak with Dr. Vegapunk since they have encountered him at various times and places. It's interesting to note that Dr. Vegapunk has no desire to dominate information. He discusses the scientist's background with the Straw Hats and presents his hypothesis of what exactly transpired during the Void Century.
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Dr. Vegapunk who leads science in the world of One Piece
After stopping Lilith, Pythagoras, and Edison from further antagonizing the Straw Hats, Shaka relays to Robin his recollection of what happened after the World Government destroyed her hometown. Dr. Vegapunk supposedly knew Dr. Clover personally, and after hearing Ohara's fate, the inventor visited the island to pay his respects. What he discovered was something else -- the archeologists' desperate attempt to save as many records as possible worked, and loads of texts were preserved in the lake. Interestingly, Dr. Vegapunk was not the only person to visit Ohara's remains. Numerous giants went to the island and salvaged all the books they could.
Another person who came to pay his respects was Monkey D. Dragon, who was still just a Freedom Fighter at the time. Dragon assured Vegapunk that the giants had pure intentions. He also showed his disapproval of Vegapunk's decision on joining the World Government. After all, Vegapunk supposedly declined Dragon's invitation to join the Freedom Fighters due to his morals. Vegapunk, however, immediately defended his decision. He reasoned that Dragon's impoverished organization would simply limit his genius. In addition to that, he was convinced that there were reasonable people within the World Government, specifically within the Navy.
Dr. Which side will Vegapunk really support in the final battle
Eiichiro Oda, the creator of One Piece, has long teased the final war's existence. It is supposed to be an event that will make the Summit War of Marineford look tame. As such, it is only reasonable to assume that all major forces in the series will be facing one another in one epic fight. Since the World Government has already turned its back on the poor doctor, it makes one wonder what faction Dr. Vegapunk will be supporting in the upcoming war. That is assuming he survives CP0's assassination attempt.
During the flashback, Dr. Vegapunk has already made it clear that he doesn't agree with the World Government's views. He only affiliates himself with them to acquire funds for his research and inventions. But since the government has put him on their hit list, that certainly eliminates them from the choices. Assuming that the doctor survives CP0's attack, then the Straw Hats may have played a major role then. Dr. Vegapunk will likely repay their kindness. However, that does not necessarily mean he will be joining their adventures. He, after all, prioritizes his inventions and research above all. What he may do for the Straw Hats, however, is mentor Franky and improve the Thousand Sunny's inventory.
The more likely option for him to choose is the Revolutionary Army. Dr. Vegapunk and Dragon go a long way back. They also share a similar vision, though the paths they've decided to take are different. Unlike the Straw Hats, the Revolutionary Army has a stationary base. Dr. Vegapunk can settle in their headquarters and even make his own lab. Since the Revolutionary Army has exponentially grown in both size and influence, they may also now have the resources to fund the scientist's works. Most of all, he must also face Bartholomew Kuma's cyborgification issue.