There are obvious villains on The Boys, like Homelander, who was able to shut down a quasi-resistance against him, as well as Billy Butcher, who might have good intentions but will stop at nothing to achieve them, including hurting others.
Alongside these two obvious rivals, each a villain to different groups, there are other more subtle villains on the show, too. It's all about perspective, and a hero to one person is a villain to another. But in a very low-key way, there are some who might not initially be on the radar as the "bad guys" for either side until after closer inspection.
Grace
Grace has done her best to help Billy and even took in Ryan to protect him once Becca died. But Grace isn't exactly an angel. In recalling her story about Soldier Boy and the incident that led to his supposed death, she mentioned how she led a group that was involved in the sale of drugs with a mandate to specifically target low-income ethnic neighborhoods.
It's true that Grace does things to benefit the greater good, burdening herself by living with the guilt of the consequences. Nonetheless, some believe that sometimes her means don't justify the end.
Starlight
There's no character as morally just, sweet, kind, and caring as Starlight. Fans adore her love story with Hughie as well. There's a reason, after all, that she polls higher than any of the other Supes, including Homelander, much to his chagrin. She's also one of the best characters on The Boys, according to Ranker. But while Starlight does everything with a soft voice and a smile, there's some villainous behavior in her.
Aside from her gathering others to try and kill Homelander, it's likely that she will continue to go against the group that has hired her on to be one of them. In the eyes of those who the vigilante group known as The Boys, Starlight is a hero for being their inside person and speaking out against injustices within Vought. But from the eyes of Vought and ers of Homelander, she's an evil detractor.
Stan Edgar
Stan Edgar comes across as the typical corporate figurehead, the man in power who may or may not be pulling all the strings. He presents every idea or order as though he is only looking out for the best interests of whomever he is speaking with, when he's clearly all about the company's interests above all else.
While he was just doing his job, there were things Stan did that were reprehensible, including using Homelander's lost childhood and insecurities against him. When Victoria – one of the best characters introduced after season 1 of The Boys - told him she realized it was her saving him all those years and not the other way around, it was made clear that Stan manipulated her as well and was finally getting what he deserved.
Cassandra
In the third season, Deep returns from the Church of the Collective, speaking out against it and deeming it a cult. But one good thing did come from his stay there: he met his wife Cassandra, who he appears to be madly in love with.
However, Cassandra might have a hidden agenda. She is seen constantly pushing Deep to bend to Vought's demands, including eating his friend (an octopus) and speaking out against A-Train. She seems more insistent that he make it back into The Seven than he is, and acts like a PR rep more than his wife. Fans suspect there might be more to her character brewing beneath the surface that hasn't yet been revealed. Nonetheless, whether Cassandra does or does not have ulterior motives, fans aren't thrilled with how she treats The Deep.
Ashley Barrett
Fans are still trying to wrap their heads around Ashley. It appears that while she does her job well, she is also always at the mercy of Homelander. Having to cower to him all the time means that she finds other ways to let out her frustrations. This often involves berating others (sometimes even using the same insults Homelander says to her) and seeking out sexual liaisons with people Vought works with.
She might come across as a sensible and intelligent person who is simply dedicated to her job. But part of that job is covering up the bad things the Supes do and work to build positive public perception around them, even though she knows the sordid truth.
Madelyn Stillwell
Madelyn came across as one of the good ones at Vought, the one who could keep the peace, including keeping Homelander in check and making sure he did what he was supposed to do. But her moves were also calculated, and she was yet another corporate figurehead who manipulated Homelander and used his vulnerabilities to make him into her puppet.
While she didn't deserve to die the way she did, there's no denying that Madelyn did deserve to be confronted for how she used and abused Homelander, all for the company's benefit, completely disregarding his feelings.
Queen Maeve
Another character who is a hero to some but a villain to others is Queen Maeve. Like her or dislike her, there's no question that Queen Maeve is one of the bravest characters on The Boys. She was the only Supe to speak up to Homelander for a long time, but like the others, she realizes she cannot beat him. She agreed to step up to be the one to deliver a blow that might eventually kill him before the big plan was foiled by A-Train.
With that said, she is supposed to be loyal to Vought and the Supes. So, the fact that she met with Billy Butcher in secret to hatch a plan against her supposed ally, even providing him with a supply of Compound Temp V, which provides 24 hours of superpowers, shows that she might not be the most trustworthy person.
Adam
Fans seem to gloss over the fact that Adam, a film director and screenwriter who has been behind many of the movies centered around and/or starring the Supes, might be representative of the stereotypical misogynistic director. This is first hinted at with his origin story script of The Seven. He pitches it in season 2 and is called out for by Stormfront due to the lack of positive, strong female representation.
But there's another interesting potential twist: keen-eyed fans have noticed that Adam bears a striking resemblance to Frederick Vought, the creator of Compound V and the founder of Vought International. Given that Frederick and his wife (Stormfront) followed Nazi ideology and created Compound V with the intention of launching a global race war, if Adam is a descendent and follows these same beliefs, he's a clear villain.
A-Train
It's easy to forget that the entire premise of the show began because A-Train was abusing Compound V, went too quickly running down the street, and tore right through Hughie's unsuspecting girlfriend. He set in motion Hughie's rage, which led to the grieving young man's meeting with Billy Butcher and determined willingness to help take down Vought and the Supes.
Through the series, A-Train continues to make bad choices, struggling to find his place knowing that he may not be able to run anymore. But his biggest betrayal was telling Homelander about Starlight's secret plan, which ensured Homelander's continued tyrannic status and resulted in Supersonic's murder. While one of the theories about season 3 of The Boys, according to Reddit, was that Homelander would take down A-Train, the fastest man may have won favor with the Supes captain by outing the detractors. To the growing resistance, A-Train is more of a villain than he might seem.