This theme is recurrent throughout the series. It is referred to frequently when Section 9 (S9) tries to find a vaccine for the stand alone complex.
It's first appearance is in Meme (season one, episode 6) where Kusanagi discovers the Delayed Action Virus infecting the security detail guarding the Superintendent General. After she discovers it she begins to suspect that a Laughing Man-type virus would manifest and attempt his assassination. She calls on Boma and Ishikawa to create a vaccine to prevent it, but this proved impossible because there was no virus to begin with. After the attempt, her and the team arrest over 30 suspects, all claiming to be the Laughing Man. Yet the creation of a vaccine continues to be part of S9's plans for preventing the stand alone complex, even into season 2. This despite Kusanagi and the team being perfectly aware of exactly what the complex is, making a vaccine an impossibility.
So then, why does it continue to be a goal of theirs?
I'd like to offer this: the Vaccine is a metaphor for a social panacea that prevents a populace from rising up against the system, keeps it in the dark and docile. People like S9 work behind the scenes to not only bring crime to justice, but also to do so in complete secrecy. A vaccine is a way of keeping the public in the dark, presumably for their own good. However, it also prevents a public uprising which could be sparked if the criminal acts of the government were made known. The Vaccine is a symbol for the current state of society. The government is always searching for ways to prevent change (it's a conservative institution by nature) and impose more restrictions on liberty (maintain power). A vaccine here would be any legislation or policy which keeps people unaware, cooperative, and/or pliant to this agenda.
On a larger scale, and probably at base, the Vaccine can come in the form of deliberately poor education and poor access to it. Public run education is fundamentally the best tool for state indoctrination (such as what we see with nationalism). Just as the state funds these institutions, it also creates the laws which determine whether public funds can go to the institution. For example, the state might have a rule that prevents it from funding parochial schools yet it may simultaneously fund schools which require the pledge of allegiance from each student. This is how the state gets involved in curricula development, controlling what people learn and thereby vaccinate them with state approved ideology/ideas/etc.
The vaccine Section 9 wants to create prevents subversives from carrying out murder, while the kind the state wants to employ would prevent S9 from even existing because S9 challenges even state criminality. The vaccines are nonetheless identical. The same power can be used for both good and evil, but what we are to learn here is that the context (the system/society) in which that power exists will determine it's use. In this case, no matter how many battles S9 wins, the war against injustice never ends in their society. The final episode is aptly titled Endless Gig for this very reason.
Kuzei is vaccinated in the final episode of season 2 while his killer says:
"Micro-machines are rather effective ...you'll have a painless death ...we view you as a dangerous element ...your country has no need of charismatic leaders that cannot be controlled ...docile consumers, that's the way to go."
He dies at the hands of an American agent, which once again brings the contrast of the threat from within to the one from without. Which is more lethal? Prime Minister Kayabuki answers this question by revealing a secret self-defense force to deter American military action. She believes the threat from without is more lethal, despite her personal struggles with opposition and corruption within her own government. Meanwhile, the Major and S9 continue to focus on those same internal threats, which is manifested in character such as Kuzei and the Laughing Man.
Kuzei's last words are "...I'll go on ...ahead." His body may have been vaccinated, but not his mind. Just as bodies belong to the state (citizenship), the mind doesn't have to. Kuzei surrenders his body back to the state, but not his mind.