It has come to the attention of the Minister of Home Affairs that Jenoma revolutionary leader Marcelo Jarti has been visiting Japan regularly every five months. Jarti is one of the world’s foremost wanted men, and has been targeted for assassination by commandos of the United States Delta Force and United Kingdom Special Air Service (SAS) a total of six times. Miraculously, he has survived each of these attempts. When Jarti returns to Japan following the most recently failed assassination attempt, Section 9 is called in to trail him and determine why Jarti has been visiting their country, with unexpected results.

Events begin to shift into overdrive after the events of "ERASER". While things seem to be going Section 9's way, people in the shadows are starting to appear.

As Motoko, accompanied by her friend Kurutan, arrives at the hospital to switch to a new prosthetic body, Togusa begins the recovery process after being wounded by the DEA's NARC Squad. However, the people still active within the NARC Squad have a few more surprises in store.

The Laughing Man returns and, just as he did six years ago, kidnaps the President of Serano Genomics without being detected. Section 9 arrives too late and sets out to find him.

Meanwhile, the Laughing Man and Mr. Serano discuss what happened six years ago. The stakes are much higher this time, and for the Laughing Man failure is not an option.

Armed terrorists have taken over the Chinese Embassy in New Port City. Holding an unknown number of hostages, the group, calling themselves the Individual Eleven, are demanding that the government cease accepting Asian refugees and dissolve the five Asian refugee camps situated throughout Japan.

The members of Section 9 have mobilized and are in position to move in. However, due to the events of the Laughing Man Incident (1st GIG), Section 9 technically no longer exists. The unit must wait for an official order from Chief Aramaki, who is busy making his case in front of the new Prime Minister of Japan.

Post Traumatic Stress Disorder is put on full display. A Japanese National named Gino, who suffered through the horrors of Non-Nuclear World War IV, the Second Vietnam War, now passes his days as a helicopter pilot for the chairman of a media conglomerate. His cushy job, however, does not take away the sheer internal pain that Gino is facing.

As he moves through his isolated existence, Gino leaps between reality and fantasy. However, he keeps his dementia solely to himself. Having no one to help him, his condition continues to worsen.