Niihama (the fictional city where our show and Section 9 are based) and Japan are under attack by a group of terrorists called "The Individual Eleven." While Section 9 re-formed after its disbanding near the end of the prior season, its clear there are still elements in the government that aren't particularly happy about its continued existence, so they have a fight on that front as well. While World War III and World War IV are mentioned, not much is said about what happened - but a lot of refugees landed in Japan. And they're a political problem that seems to be tied in to "The Individual Eleven." The season concentrates on moving the season's story arc forward in every episode: there's very little in the way of filler (there was a lot more in the first season).
Not that it doesn't have its flaws: the series is prone to convoluted plots by the bad guys, and fairly regular wild leaps of logic by the authors who take it as a given you'll accept what you're told as a fait accompli even though they didn't really lay the ground work for it ... and despite the fact that a good portion of the series is asking you to think and use your deductive reasoning ... At least this season Kusanagi isn't quite as obviously wearing a one piece bathing suit as a "uniform," although they haven't stopped the fan service ... <sigh>
Overall, a better season than the first.
Two movies were released around the time of these two seasons: "Ghost in the Shell: Stand Alone Complex - The Laughing Man" and "Ghost in the Shell: S.A.C. 2nd GIG – Individual Eleven". The first appears to be the first season cut down to focus on the material about the Laughing Man, with a run-time of 2h40m, and likewise the second is the second season focused on the political events and the "Individual Eleven," also running roughly 2h40m. Wikipedia says they have some original content, but I skimmed both and saw so little that wasn't in the TV series that I ignored them.