Most stories within the superhero genre have the hero interact with some segment of the government for various story reasons. Some have the hero work very closely with the local police. This relationship can be either tenuous or well-established, but other characters within the story will hold different opinions on whether this relationship is legitimate, and often the threat of a rift in this relationship is threatened to increase the drama of the story. Other stories will have the hero in direct conflict with local authorities, and the threat of being arrested as a criminal, as they are trying to do good, will be a consistent element of the hero’s story.
While several various examples can be brought to mind, there is no standard formula for this relationship between the main hero and civil authorities. However, it is often informed by the kind of character that the story is trying to portray and the author’s views on authorities. Many authors who come from cultures where the government and civil authorities are honored and respected depict the superhero as someone who answers to the government (like they have special permission or authorization from a government agency) if they are not already an official agent of a government agency. If an author is critical of government agencies, they can have the hero oppose them as a vigilante. All this is further dependent on the type of story that the author wants to tell.
I think a nuanced middle depiction has more storytelling opportunities than a one-sided depiction that either holds government agencies as idealized systems or as wholly corrupt and untrustworthy. Although an extreme depiction of the government can be suitable for a fictional world, it can take away from a story’s realism.
One plot device that has become famous in the last couple of decades is the idea of the government insisting on the hero or heroes of the story registering with the government and becoming a federal agent. One reason this plot element is used is that it allows the author to use the story as a parallel to various political climates. The author always has the right to make this kind of creative choice, but sometimes it feels like a tone shift or a departure from previously established worldbuilding. The introduction of this element after the fact usually requires some kind of disaster or other event to trigger a change in the perspective of the characters. If the audience can’t be convinced that this plot element is a logical result of the triggering event then it feels artificially inserted, and the parallels that the author wishes to make with the story or the dramatic tension that they are trying to cultivate can feel weak.
Though this trope does prompt the audience to think about how these fictional elements would be received in a realistic setting, I find the trope triggers more inconsistencies than it prompts introspection. Characters that are already established in their genre’s give the audience’s clues on how they would respond to this kind of dilemma before it arises. This makes it very hard for the story to have any dramatic tension about which choice the character will make. The audience already knows what will happen. The only conflict that can be generated is between characters that we know will disagree on the issue, and have probably already clashed over other past issues. Thus in most cases this trope only serves as another set dressing for character conflicts that have already been shown in the story. It seems to function as an excuse for turning what would be a verbal discussion or debate, maybe even an argument, into a more actiony fight sequence. It can certainly be spectacular, but it seems like a flimsy excuse to me.