In the year 2029, the world is made borderless by the net; augmented humans live in virtual environments, watched over by law enforcement that is able to download themselves into super-powered, crime busting mecha.

The ultimate secret agent of the future is not human, has no physical body and can freely travel the information highways of the world, hacking and manipulating whatever and whenever required.

The agent, created by the Ministry of Foreign Affairs, is designated code name Project 2501 and distanced from them under the pseudonym "The Puppet Master." 2501 seems to be the perfect solution to their international espionage requirements. Everything runs smoothly until this prototype virtual agent concludes it is a life form in its own right "born in a sea of information" and requests political asylum and true physical existence in defiance of its creator.

The race is on to recapture the Top Secret Project 2501 before it succeeds in finding a host body and escapes for good. What the Ministry of Foreign Affairs hasn't counted on is the Puppet Master's cunning and reserve. It has threatened to expose their illegal creation (itself) to the Internal Bureau of Investigations who are unaware of its source, and regard the Puppet Master as a Grade A priority security threat. The two agencies maneuver discreetly against one another in a violent, high-tech race to capture the ever changing omnipresent Puppet Master.

The Internal Bureau is unaware of the Puppet Master's persuasive ability to offer seductive hints at true freedom to their semi-cybernetic human agents, who are forced to question their own validity as human beings. One of these agents, Major Motoko Kusanagi, is a highly trained female agent sent to counter the Puppet Master's threat, will have to make the ultimate decision when the Puppet Master suggests a merger with her.

While the Ministry of Foreign Affairs and the Internal Bureau of Investigations are engaged in direct explosive confrontation, Kusanagi must decide if she will fulfill the Puppet Master's ultimate objective to become truly human and exist outside of the Electronic Net.