Synopsis:

In 2029 a sentient computer virus is smuggled into an unspecified country. Several prominent scientists from the project also try to defect. Meanwhile, Major Motoko Kusanagi, a cyborg agent with the government's secret Internal Affairs team “Section 9,” is troubled by a series of crimes committed by the Puppet Master – a terrorist who hacks into the minds of innocent citizens.

The Puppet Master proves difficult to track – leaping from the brain of a ministerial translator to a humble garbage man, to a small-time criminal. Though all the suspects are eventually apprehended, they are mere shells – the crucial soul, or “ghost” of the Puppet Master has already found a new host by the time the squad arrives.

In fact, the Puppet Master is not a foreign criminal at all, but a creation of “Section 6,” a rival espionage wing with the Ministry of Foreign Affairs. Section 6 has been using the Puppet Master to create terrorist incidents and crimes that are then used by the government to justify unwelcome new policies and laws, but the artificially-created intelligence has now turned on its former masters.
 
The Puppet Master asks for political asylum, but its latest body (a new cyborg fresh off the assembly line) is stolen by agents of Section 6. Kusanagi and Bateau track it down to a remote location, where a gravely wounded Motoko is finally able to link with the Puppet Master. She has become troubled by the false memory incidents around her, and wants to question it about what makes it “sentient.”

The Puppet Master reveals that to truly be alive, it must gain the ability to reproduce and die.  It proposes that the two of them merge their souls to form a new being…