First season focused on the Laughing Man and his imitators (ultimately including politicians and companies that used him as a scapegoat to hide their own dirty laundry). Season 2 was the one that focused on the "Individual Eleven".
Ok, recap: Ghost in the Shell focuses on a Japanese intelligence department that operates under the Ministry of Home Affairs, known as Public Security Section 9. They are extremely skilled, have broad discretion and minimal oversight or public awareness in accomplishing their duty, making the most obvious parallel the Impossible Mission Force of Mission Impossible. Their focus is serious cyber crime, high profile murder cases, and unlawful acts from public officials.
During the first season, a lot of their efforts are focused on investigating the elusive Laughing Man, only for them to slowly realize that he wasn't a criminal mastermind or terrorist leader, but rather a one-off event with everything afterwards that was attributed to him being the work of copycats, including various companies and government officials to mask their own illegal acts. Section 9 ultimately discovered that the Secretary General was actually the one pulling the strings for the corporate terrorism that had been using the Laughing Man scandal as a smokescreen.
The Secretary General learns about this and leaks information to the press to cast Section 9 in a bad light before abusing the law to get Section 9 shut down, branding them as dangerous radicals in an effort to assassinate them and re-bury the evidence. This is done even as Aramaki is presenting the same evidence to the Prime Minister...who is incapable of taking action because it's immediately before the elections and the Sec-Gen's party would turtle up and stonewall any efforts to hold him accountable. Post-election, the PM discloses the evidence to the public, pegging the Secretary General as the ringleader of the Laughing Man scandal.
The actual Laughing Man was an anonymous hacktivist whose crime of passion was the incident that defined the Laughing Man's image. They do offer him a job for his hacking expertise, but on scale, that's no worse than the FBI doing the same with Frank Abagnale for his forging expertise.