A genius par excellence, Dr. Vegapunk was one of the most enigmatic figures in Eiichiro Oda's One Piece for a major portion of the story till date, with his true appearance only being revealed in the Egghead Island Arc of the Final Saga. His name had been mentioned by several characters at various points in the Straw Hats' journey, with some regarding him as an individual to idolize, possessing an intellect without equal, whereas others see him as a mad scientist whose work leaves nothing but death and destruction in its wake. Thus, he remains a divisive figure, but his contributions to scientific advancement in One Piece cannot be discounted by any means. While spearheading the secret research group MADS, Vegapunk and his associate, Vinsmoke Judge of the Germa Kingdom, were the ones who discovered the Lineage Factor, described as "the blueprint of all life."
This revolutionary breakthrough paved the way for Artificial Devil Fruits, Modified Humans, Cloning, and super soldiers such as the Pacifista, and their successors — the Seraphim. In this vein, Vegapunk has been responsible for some of the most fearsome weapons used by the World Government. Since his first appearance, Vegapunk has always presented himself as a pacifist, whose work is motivated by a genuine desire to advance civilization and improve lives, and this has been verified by many of his friends, and allies. However, his inventions are often used to do more harm than good, which says a lot about how much he truly cares about the consequences of his actions. When considering that he is a character that many — including the Straw Hats' shipwright Franky — look up to, and strive to emulate, the conundrum of whether the genius scientist's pacificism is genuine or not, is not one with a simple solution.
Producing Results At Any Cost
Vegapunk has an idealistic side to his persona, one that will never allow the use of children in gigantification experiments, the release of poisonous gases in tests for fear of it harming innocent civilians, or the creation of weapons of mass destruction. While he has been able to prevent the first two calamities form occurring, he can also be overly focused on obtaining results without any concern for the manner in which his inventions are used.
The genius scientist had a hand in the creation of both the Pacifista and the Seraphim, and these two creations are capable of bringing about the very destruction he sought to prevent. It is no surprise that Vegapunk is such a perfectionist who is intensely driven to achieve his ambitions, but he often seems to neglect the fact that all of it comes at a cost. He often becomes hyper fixated on certain things and will refuse to let go of his desire, regardless of the toll it takes on him and his subordinates. This includes projects such as his endeavor to determine the weight of the human soul, or to recreate Kaido's Devil Fruit with the aid of his Lineage Factor.
In these cases, he is quite relentless and unyielding in his pursuit of truth, and will not back down until his scientific curiosity is satisfied. While these can be admirable qualities, and have contributed to his success, they can also manifest in a more malicious manner. Vegapunk is also not above stealing from others to fund his research, and openly proclaimed that he only chose to ally with the World Government due to the resources they were able to provide in order to further his research.
Aiding The World Government
As the head of the Marines SSG (Special Science Group), Vegapunk's duties involve the research and development of advanced technology and weaponry to aid the World Government and its military. He was drafted into this role after being arrested for his involvement in MADS, and elected to work for the World Government in order to secure funding for his research. It is certain that Vegapunk is well aware of the dangers of his research falling into the wrong hands. This is evident in how he concealed his knowledge of the information stored in the library of Ohara, particularly regarding the Void Century.
Although the island was destroyed over 20 years ago, Vegapunk successfully kept quiet in fear of becoming a target of the World Government, as he was the only one who knew about the research into the Void Century that was being done on Ohara. This act on its own is quite commendable, as he sought to preserve and replicate the work of the scholars of Ohara, with his mind being the only remaining record of their work after the destruction of the Tree of Knowledge. This eventually led to the order for his execution, once the government learned of his research into the Void Century, which they viewed as a threat and sought to snuff out as soon as possible.
However, his decision to use some of this research to create weapons of mass destruction for the World Government negates this, as he used the scholars' knowledge to bring about the exact outcome they feared. This puts his pacifism, awareness, and his sense of morality under question, as he was conscious of the World's Government's intent in recruiting him and still chose to aid them, knowing full well that his creations would only be used to bring death and destruction to all who opposed his employers. On the other hand, he had no alternative, as denying the World Government's requests would have amounted to a death sentence, regardless of how valuable he was as an asset.
Creating Instruments Of Oppression
One of the biggest contradictions in Vegapunk's pacifist persona, is his work in developing the World Government's three most feared weapons. In order of their introduction, they are: the Pacifista, the Seraphim, and the Mother Flame. While the first two among them have been instrumental in the dismantling of the Shichibukai system, they are also incredibly potent weapons who could cause immense loss of life if they fall into the wrong hands. The World Government itself may not be the ideal handlers of such powerful instruments of destruction, considering their track record of using deadly force to deal with dissent of any kind.
This, coupled with the fact that Vegapunk chose to create them, with complete knowledge of the intent behind developing them speaks volumes of how little he actually seems to care about how his work can be used to spread tyranny and oppression, even if his original intentions were less malicious. All this pales in comparison to the Mother Flame, a super weapon developed by him for use by the Five Elders. Boasting destructive capabilities that seemingly have no limits, this invention is able to destroy entire islands instantly, leaving no trace of their existence.
Its first appearance in One Piece, was shortly after the Levely, when Imu commanded the Five Elders to use it to wipe the entire Lulusia Kingdom off the face of the planet. Such a weapon is perfectly suited to the World Government's campaign of silencing the truth about the Void Century, and they were able to deny the existence of this kingdom immediately after this destruction. Even if Oda does reveal some hidden intention behind his efforts in delivering such a weapon to the World Government, the fact that he was culpable in committing such an act of genocide, signifies that Vegapunk's facade of pacifism is not a true indication of what he really thinks, proving that actions speak far louder than words.