Complex sentence: Daisuke Aramaki, the head of Section 9, suspects that the project and the Puppet Master were tools of the Ministry of Foreign Affairs, and that the escape might lead to revealing secrets that could embarrass both Section 6 and the ministry.
Split into simpler sentences: Daisuke Aramaki, the head of Section 9, suspects that the project and the Puppet Master were tools of the Ministry of Foreign Affairs. The escape might lead to revealing secrets that could embarrass both Section 6 and the ministry.