The World Government is the biggest and most powerful organization in One Piece. It was established by the twenty rulers many centuries ago. They allied together to ensure that they could overpower the Great Kingdom and erase it from existence. The twenty countries were successful in their objectives, after which they successfully formed the World Government.
The rulers of each country decided to settle in Marijoa, and they eventually became Celestial Dragons. As the monarchs started living in the Holy Land, the countries that they left behind adopted new royal families. Any records containing information about the previous rulers were erased by the World Government. This ensured that the identities of the monarchs remained hidden and that no One Piece criminal would target them in the future.
The Empty Throne
The Empty Throne symbolizes that all the rulers were equal and that they would not seize all the power for themselves. They also placed their swords around the throne as a sign of their loyalty. Considering the fact that there were twenty rulers who allied together, there should be twenty swords around the Empty Throne. Instead, there are only 19 swords. The missing sword belongs to Nefertari Lily, the queen of Alabasta. She ruled over the country and sided with the other countries. Unlike the other leaders, she did not stay in Marijoa. She allegedly went back to her kingdom to rule it, which would explain why the Nefertari family still holds all the power in Alabasta.
In Chapter 1084, Cobra stated that Nefertari Lily never went back to Alabasta. It was her younger brother who ruled the country. The Five Elders refuted his claims and told him that there was absolutely no doubt that she returned to her homeland, although they no longer had the evidence to prove it. Cobra was dissatisfied with the answer, but he had no other option. Before the end of the chapter, Imu climbed the stairs and sat down on the Empty Throne, shocking the Five Elders and Cobra.
The Missing Sword
The absence of the sword could mean two things: 1. Lily didn't want to continue being a part of the oppressive regime of the World Government. 2. She is actually the true sovereign of the World Government, and she has taken up the name "Imu." The second idea seems far-fetched, but it wouldn't be wise to rule out the possibility entirely; after all, the silhouettes of the two characters have some resemblance. Imu doesn't appear before just anyone, and to do so after Cobra mentioned Lily makes things even more interesting.
The possibility of Lily withdrawing her support for the World Government is the likelier outcome. She could have found out about Imu's existence and their plan to rule the world. This would have made Lily realize that she and the other monarchs were tricked into destroying the Great Kingdom when it posed absolutely no harm to them. Lily's decision could have induced panic in Imu, who wouldn't want the truth to come out. So the ruler of the world decided to eliminate Lily and tie up any loose ends.
The Role of The Nefertari Family
By now, it is fairly obvious that the Nefertati family will have a crucial role to play in One Piece. The Nefertari family has safeguarded a Poneglyph for generations. They wouldn't do such a thing, especially when the Poneglyphs are the bane of the World Government. This implies that Lily and her younger brother were probably aware of the Poneglyph's importance, and instead of reporting it to the World Government, they decided to protect it. The next few chapters should contain more information about Nefertari Lily and why she decided to abandon her position.
It will also be interesting to see the discussion between Nefertari Cobra and Imu. It definitely seems that Cobra is going to learn about something big that could shock the entire world. However, the information will come at a high price, and Cobra will be murdered by the World Government. It has been implied that Sabo knows about the death of the king of Alabasta. The Revolutionary Army member was in and around the Lost Chamber, and based on the guards' conversation, it contains some major secrets. Sabo very likely went to the room and, after poking around for a while, found that it was linked to the Empty Throne room.
Another thing to keep in mind is that the World Government is chasing Vivi and Wapol, which has been confirmed by the latter. The two were last seen traveling aboard Morgans' ship as they had to get away from Marijoa. Wapol said that the World Government would kill them if their location was disclosed. This implies that Vivi and Wapol must have seen something that they shouldn't have. It is possible that they may have been around the place where Cobra was killed, and Vivi might have screamed after seeing her father murdered before her eyes.