Master, Kusanagi's team follows the traced telephone calls that sent the virus. After a chase, they capture a garbage man and a thug. However, both are only ghost-hacked individuals with no clue about the Puppet Master, where the investigation again comes to a dead end. Megatech Body, a shell manufacturer with suspected close ties to the government, is hacked and assembles a shell. As it escapes, the shell is hit by a truck. As Section 9 examines the shell, they find a human ghost inside it. Unexpectedly, Section 6's department chief Nakamura arrives to reclaim the shell. He claims that the ghost inside is the Puppet Master himself, lured into the shell by Section 6. The shell reactivates itself, claims to be a sentient being, and requests political asylum. After the Puppet Master initiates a brief argument about what constitutes a human, a camouflaged agent accompanying Nakamura starts a diversion and steals away the shell. Having suspected foul play, Kusanagi's team is prepared and immediately pursues the agent. Meanwhile, Section 9 researches "Project 2501", mentioned earlier by the Puppet Master, and finds a connection with Daita, whom Section 6 tries to keep from defecting the country. Facing the discovered information, Daisuke Aramaki, chief of Section 9, concludes that Section 6 created the Puppet Master itself for various political purposes, and now seek to reclaim the body that it currently inhabits. Kusanagi follows the car carrying the shell to an abandoned building, where it is guarded by a robotic, spider-like tank. Anxious to face the Puppet Master's ghost, Kusanagi engages the tank without backup, resulting in her body being mostly dismembered. Her partner Batou arrives in time to save her, and helps connect her brain to the Puppet Master's. The Puppet Master explains to Kusanagi that he was created by Section 6. While wandering various networks, he became sentient and began to contemplate his existence. Deciding the essence of life is reproduction and mortality, he wants to exist within a physical brain that will eventually die. As he could not escape Section 6's network, he had to download himself into a cybernetic body. Having interacted with Kusanagi (without her knowledge), he believes she is also questioning her humanity, and they have a lot in common. He proposes merging their ghosts, in return, Kusanagi would gain all of his capabilities. Kusanagi agrees to the merge. Snipers from Section 6 approach the building,