The World Government controls over 100 countries, making it the biggest organization in One Piece. Since its inception, it has continued to expand by offering the governing kings certain amnesties. The World Government has maintained a charade of being the good people, but that's very far from the truth.
In order to maintain its grip over the world, the organization has tried every underhanded trick. It has laid waste to entire countries under the guise of justice. In other cases, it has eliminated individuals of extreme importance. With that in mind, here are the most influential One Piece characters that have been murdered by the World Government.
7 Nefertari Cobra
Nefertari Cobra was the ruler of Alabasta. He was an honorable and wise man who loved the people of the nation. Cobra always based his decisions on how they would help the people of Alabasta to live a peaceful and good life. After nearly losing Alabasta to Crocodile, Cobra put in an incredible amount of effort to restore the country to its glory.
As the monarch of Alabasta, Cobra attended the most Reverie along with his daughter, Vivi. He also scheduled a meeting with the Five Elders and asked them some very testing questions. Cobra even managed to see Imu, the true sovereign of the world. It is likely that he was murdered because he learned about Imu's existence.
6 Gol D. Roger
Gol D. Roger is the only person to have ever been called the King of Pirates. Roger and his crew traveled to Laugh Tale, where he found the One Piece and learned the actual truth about the world. After his successful endeavor, Roger surrendered himself to the Marines.
The World Government was pleased to have gotten its hands on the Pirate King, and immediately announced his execution. People throughout the world gathered to see Roger's execution in Loguetown, where he unexpectedly revealed that he left the greatest treasure in the Grand Line. Following his execution, the World Government placed its focus on changing his name to Gold Roger to hide the "D."
5 Clover
"Knowledge is power" is quite a famous saying, and it holds true in the world of One Piece. The World Government is built on lies, and it has done everything in its power to protect its secrets. One of the main laws that they implemented was not allowing anyone to read the Poneglyphs.
These massive stone pillars have been inscribed with information about the Void Century, Laugh Tale, and other things. However, not every person is willing to obey the rules. The scholars of Ohara were the first major group to indulge in the reading of the Poneglyphs. They spent a long time learning the language inscribed on the Poneglyphs. With the newfound information, the scholars learned about the true nature of the World Government. Clover was the leader of the group, and it was under his guidance that the scholars discovered the truth. The Five Elders realized that they could not let Clover live, so they ordered the agents to kill him.
4 Joy Boy
The Great Kingdom existed before the Void Century. According to the limited information, it was an incredibly powerful country that had made many advancements in science. It is unknown what kind of people lived in the Great Kingdom, but the World Government considered them a serious threat.
Many popular theories purport that Joy Boy was from the Great Kingdom. He fought to protect his nation from destruction, but sadly, he failed. The World Government erased almost all the traces of the Great Kingdom and Joy Boy as well.
3 Rocks D. Xebec
Rocks D. Xebec was a legendary pirate who lived many years before the current timeline. He was a fearsome man who was hellbent on ruling the world. In order to achieve his goal, Rocks recruited many powerful people to his crew. The crew's name became known far and wide, and they were considered dangerous. The World Government knew about Rocks' ambitions, and it couldn't let such a thing happen.
So, the Marines allied with the Roger Pirates to take down the Rocks Pirates. The fight took place at God Valley after Rocks and his crew attacked several Celestial Dragons and their slaves. In the end, Rocks was defeated, and his crew disbanded. Both Rocks and the God Valley disappeared afterward, so it is plausible to assume that the pirate is long gone.
2 Nefertari Lily
Nefertari Lily was the ancestor of Nefertari Cobra and Vivi. She ruled over Alabasta almost 800 years ago, and she was one of the twenty rulers responsible for the creation of the World Government. After the group's success, almost all the monarchs stayed in Marijoa and became Celestial Dragons— everyone except for Lily, who decided to go back to Alabasta.
It is shocking to think that a person would give up such an opportunity without any good reason. Lily might have figured out the truth about the World Government and Imu. So she decided to head back to Alabasta, where she would be safe. Unfortunately, she was murdered before she could reach her country.
1 Portgas D. Ace
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Ace was the son of Gol D. Roger and Portgas Rouge. He took his mother's name because he resented his father. Despite frowning upon his own existence, Ace continued to live, and eventually, he became a great pirate. Whitebeard was so impressed with his resolve that he offered the young pirate a place in his crew.
Ace quickly rose through the ranks and was named the Second Division Commander of the Whitebeard Pirates. According to Sengoku, Whitebeard wanted to make Ace the Pirate King. Ace had many qualities that made him a threat to the World Government, which is why the organization risked going to war with Whitebeard to kill him.