I'm liking the theory that Vegapunk gives Bonney his control of the Seraphim more and more.
"Here is my authorization chip, Bonney. I want you to control the Seraphim. A kind girl like you, will help them to become good-hearted individuals. I don't expect to be forgiven, for the things I've done. All I can ask, if that you let me live long enough, to help bring about the peace your father gave his life up for. Once we leave Egghed... I'll tell you, why your father agreed to give up his body to science and the government."
"Here is my authorization chip, Bonney. I want you to control the Seraphim. A kind girl like you, will help them to become good-hearted individuals. I don't expect to be forgiven, for the things I've done. All I can ask, if that you let me live long enough, to help bring about the peace your father gave his life up for. Once we leave Egghed... I'll tell you, why your father agreed to give up his body to science and the government."