The Boys season 2's ending sets up season 3 to copy the MCU's Captain America: Civil War event in a particularly clever way. Having been mostly focused on copying the DCEU - including parodying Joss Whedon's Justice League reshoots - the irreverent superhero show looks like it will now take aim at Marvel's behemoth franchise.
Season 3 of The Boys is set up to be a huge and potentially volatile event. The ending of the second season leaves The Seven as they were no more, with Homelander all-but replaced as the leader thanks to Queen Maeve's blackmailing and A-Train invited back in. Then there's the issue of Homelander's son and his relationship with Billy Butcher, plus the fallout from Stormfront's exposure and defeat. On top of that, it's also already known that Jensen Ackles' Soldier Boy will be this universe's de facto Captain America parody (with a far darker edge no doubt, given the show's usual creative tendencies). Add to that Hughie's defection from The Boys to join Victoria Neuman's Office of Supe Affairs and there is very much a sea of change.
That last point is one of the most intriguing because it sets up a fracture in one of the key relationships that have underpinned the first two seasons of The Boys: the dynamic between Hughie and the other Boys. Previously, Hughie had already displayed major dissent to Butcher's approach to dealing with superheroes, and now that Hughie has effectively picked a new side that doubles down on his own intent to "do the right thing", The Boys has its own set-up for a Civil War-like event. Not only was there a trigger event that will change public perception of superheroes, but there is now ideological conflict in how superheroes should be managed and similar potential for emotional fall-out (not just between Hughie and Butcher, but Hughie and Annie too).
While the set-up may not result in Hughie and Butcher running at each other across an airport and fighting, The Boys' Civil War could be just as disastrous for the central relationships in season 3. Hughie secretly choosing to join Victoria Neuman's government office behind Butcher's back puts him at odds with how The Boys operate. There's limited chance Neuman will allow Butcher to continue operating and Hughie choosing to do things by the book draws a line under what he truly thinks of The Boys and Butcher too. And given the fact that Butcher is right in his assertion that supes require extra-legal solutions to their own extra-legal activities (albeit with the caveat that his methods are often over-zealous), it's equally as unlikely that Butcher would allow himself to be recruited to follow any sort of accords. And The Boys are a superhero team too, thanks to Kimiko's presence - not to mention the fact that Frenchie, Butcher, and MM's special skills all qualify them as much as Tek Knight's resources - so they would be forced to toe the line too.
Because of Homelander's volatility and the fallout from the revelation of Stormfront's past (and the gravity of what she almost achieved), it's likely that Neuman's office will be far more prominent. Given that Neuman herself has some - as yet unrevealed - ulterior motive for her government involvement, involving herself with The Seven and The Boys makes sense, which will put her new underling, Hughie, at odds with both Butcher and Starlight. She may be more idealistic than her fellow Seven members, but Starlight has shown that she's willing to go beyond the law and the natural extrapolation of what the Office of Supe Affairs stand for is superhero accountability and regulation. Starlight has profited too much from underhand and downright criminal activity so far for her to roll over and accept that and season 3 of The Boys could end up pitting Hughie against an unlikely alliance of Butcher and Starlight as they both work to stop Neuman controlling supes to her own nefarious end. In this strange new dynamic, Hughie is Iron Man, with the trauma of his lost loved one guiding his ideology, and Butcher and Starlight are Captain America's stand-ins, firm in their belief that any sort of superhero regulation is wrong. It could all be fascinating.