Transgenderism
The central thematic concern of the story is the complex issue of what makes up identity. Nimona herself is the embodiment of this complexity as a result of her ability to shapeshift.
The Power of Government Propaganda
The Institution of Law Enforcement & Heroics is invested with the trust of citizens on the issue of determining the difference between heroes and villains. The Institution has castigated Ballister Blackheart as a supervillain when, in reality, he more strongly adheres to an actual code of honor than the self-identified heroes working at the Institute. Propaganda has served to create stereotypes without foundation. Ambrosius Goldenloin is hailed as the ultimate hero the Institution has created, but he actually has a more ambiguous morality than Ballister though, admittedly, Nimona's morality is even more ambiguous than Goldenloin's. The single most villainous character in the story is the head of the shadowy Director of the Institution which promotes its own heroic defense of law and order.
Subverting Stereotypes
The story opens with Nimona lying to Ballister about the Institution sending her to take on the role of his sidekick and identifying him as the biggest name in supervillainy. Eventually, Ballister will confound expectations by insisting that there are rules which must be obeyed even in the service of villainous actions. The line between hero and villain is blurred to the point of completely subverting the roles as Ballister becomes heroic and the Institution is revealed to be corrupt and villainous. Even more subversive, however, is that by the time the story concludes, Nimona has proven herself to be not the sidekick in this adventure, but a figure far more feared and dangerous than Ballister himself. On a more specific level, the notion of heroism is also subverted when it is divulged that Ballister and Ambrosius share a romantic past together, thus undermining the stereotypes of both warriors and homosexuals.
