The information from the body lead Section 9 to uncover the mysterious Project 2501 . Section 6 claim the project was created to catch the hacker , but it was initiated before his appearance . Section 9 speculates that the project itself created the Puppet Master , who then escaped , and Section 6 now want him back . Daisuke Aramaki , head of Section 9 , suspect that the project and the Puppet Master are tools of the Ministry of Foreign Affairs . The escape might lead to the release of secrets that could embarrass Section 6 and the Ministry .