You know the score. In 2031 AD Japan's Public Security Section Section 9 is tasked with investigating cyber-crimes.
This season takes up some months after events in the first season. The team is still disbanded and hasn't yet officially been reinstated as a police entity.
Japan is being flooded with Asian immigrants fleeing the politically and economically chaotic post-war conditions on the mainland. The tension gives rise to the Individual Eleven, a group of anti-immigrant radicals bent on affecting the ouster of all the immigrants. They start by taking hostages at the Chinese embassy. Section 9 is taken out of limbo and put on the case.
The plot(s) soon thicken as the team has to contend with a plan to kill the Prime Minister, a nuclear device or two, and a mysterious government liaison who has an agenda of his own. The Individual Eleven's activities turns public opinion and government policy against the immigrants who quickly become radicalized and threaten to declare autonomy if the government tries to deport them. When one of the Individual Eleven, a man who Kusanagi later discovers she had a past with, decides to become the immigrant's leader, things only get more complicated.
This mission also marks the change in Kusanagi's personality as she changes from the no-nonsense, but still amiable person she was last season, and starts her slow descent into the morose, self-hating sadsack she will become by the time of the 1996 GITS movie.
Like season one the episodes are split into "stand alone" episodes; episodes not dealing directly with the season's overarching storyline, and "complex" episodes; episodes that are part of the season's overarching story. Sometimes this is bad, other times it's good.
For instance, this season we are formally introduced to the American Empire, an entity that formed after the last world war. It is comprised mostly of the former Confederate States of America, whose territory includes Washington DC and CIA headquarters in Langley, VA.
The first episode featuring the AE has two Japanese-American CIA intelligence officers who show up to help catch a psychopathic American GI who is serial-killing women in Japan. Needless to say the series treats the Americans with the same contempt as a James Bond movie, only it equates less morality to them. America bashing is a recurring theme throughout the season.
This kind of stand alone episode is fine since it's a good episode and ties into the tale as the American Empire becomes a greater part of the Individual Eleven investigation.
Hell, I even like the episodes where Saito and Paz reveal their backstories. Kusanagi and Aramaki's British adventure is a stretch but still a good episode.
What I didn't like as much were stories like when Togusa goes to court for shooting a perp, or when the team investigates a deranged pilot, or Batou and Kusanagi go to Germany to stop a "terrorist." The series has to pause several times so they can go on these unimportant sojourns.
The show's producers didn't seem to realize that the stand alone episodes simply weren't as interesting as the complex ones. If they had chosen to focus instead on Gouda's background or the members of the Individual Eleven, or even what the hell Section 9 was doing between seasons one and two, that would have been FAR better.
This season has the same creative team as the first, including Yoko Kanno, whose music has only improved.
I prefer this season's storyline to the first. It does what SAC does best-- straight-forward crime solving and action, emphasis on the "straight-forward" part. The stand alone episodes tend to hurt the pacing but it's still a great GITS series.