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The final defeat of Homelander doesn't necessarily mean supes are done for good, but Hughie reveals the CIA will never allow a superhero comeback. This is especially true after the events of the "Dear Becky" epilogue, which takes place a decade after the main series.
The Boys' very public final battle against Homelander and his uprising of supes firmly turned the tide of public opinion against its former "heroes." This is because Homelander's actions, including a violent coup at the end of the main series, destroyed the public's faith in the idea of superhuman protectors. Homelander's actions were so damaging that they destabilized the entire superhero system, leaving those that did remain no viable foothold to make a comeback. In a way, this also adds another dimension to the tragedy of Billy Butcher's final villainous turn.
Butcher's plan to commit genocide was always painted as a horrific and unjustifiable reaction to what he saw as the cancer of superhuman supremacy, but "The Boys: Dear Becky" also confirms it was unnecessary. The story emphasizes that Homelander's actions were damaging enough to destabilize the entire superhero system, leaving those that did remain no viable foothold to make a comeback. In other words, "The Boys'" typically grim vision of American politics shows that with Homelander off the board, the existing power structure would be more than capable of suppressing what it came to view as a threat.
"Dear Becky" offers one final chapter in the bloody tale, set over a decade following the conclusion of the main series. The tale sent protagonist Hughie on one last adventure, investigating the source of a mysterious journal detailing the earliest days of the Boys. As part of the story, fans were offered a glimpse of a world where "superheroes" no longer exist, leaving fans with the implication that even if a new generation of supes were to one day rise, the world would never let another Homelander happen.
In "Dear Becky", Hughie reveals that the CIA will never allow a superhero comeback. The CIA subtly destabilizes groups that support supes by sowing confusion and dissent among them, and the Boys' job is now done almost exclusively online. This means that even if a new generation of supes were to emerge, they would never be able to achieve the same level of power and influence as Homelander.
The idea that over ten years later, the world would still remain resolute that supes not be given unchecked power ever again, is effectively as close to a happy ending as "The Boys" was ever likely to get. Even as some characters are depicted in "Dear Becky" inevitably plotting a supe revival, the comic series' final note makes the prospect seem unlikely.
It is not that a powerful Superman-analogue could not be born, but that they would never be idolized and venerated by an unwitting populace, as Homelander was for so long. This is the ultimate legacy of superpowered characters in the series, one of a brutal fall from grace. As "The Boys" epilogue series made a point of emphasizing, even a pessimistic view of the future didn't involve the return of supes to any level of prominence.