The following contains spoilers for The Boys Season 3 finale, "The Instant White-Hot Wild," now streaming on Prime Video.
Season 3 of The Boys makes a radical change from previous seasons by pitting its titular plucky heroes against each other, splitting Butcher and Hughie off from the rest as they team up with the recently awoken Soldier Boy to try to kill Homelander. Both Mother's Milk and Starlight see this for the devil's bargain it is, and try to stop them. Frenchie and Kimiko join them later, with Frenchie's own objection centered on his desire to stand up to Butcher. That seems like a fairly simple conflict, but it only gets more complex as the season goes on, with more and more switches of allegiance and uneasy alliances.
Everything begins to go off the rails at the end of Episode 7, "Here Comes a Candle to Light You to Bed." Soldier Boy calls Homelander after learning he's the other supe's father. They don't exchange many words, but it's clear neither can be fully relied on to kill the other. Homelander even goes so far as to kill Black Noir, murdering his oldest and most loyal ally because of a secret Noir didn't ever think would be relevant. Soldier Boy doesn't do anything nearly as drastic, but his torn monologues to Butcher about his own father show how he's conflicted.
Butcher joins back up with the rest of The Boys briefly during the season's finale, seeming for a moment to acquiesce to their plan of incapacitating Soldier Boy instead of letting him kill Homelander. They're interrupted when Maeve destroys the neurotoxin they'd planned to use, forcing them back into a locked room. Butcher and his two compatriots leave, and square up to fight Homelander when they arrive at Vought Tower, but stop when they realize Homelander's brought Ryan to the tower. Suddenly Butcher's preferred outcome, the entire tower collapsing and everyone dying, isn't acceptable to him.
So he switches sides, and starts fighting alongside Homelander to take out Soldier Boy and Maeve. Kimiko, Starlight and Mother's Milk arrive moments later, helping to try to pin down Soldier Boy, with even Maeve realizing he can't be allowed to hurt anyone else and tackling him clear through a window in a sudden act of heroism. This is a messy, quickly changing web of loyalties, but The Boys makes all of it work by clearly setting up why each character acts the way they do.
The Boys isn't some cloak-and-dagger game of intrigue. Characters don't always act out of self-interest or a need to accrue power. They make the choices they do because of what's important to them. Butcher wants to kill Homelander because he feels the supe is responsible for his wife's death, but swore an oath to her before she died that he would keep Ryan safe. The second Ryan's life is in danger, he does everything he can to protect him. That even means working with Homelander, because the need to save Ryan trumps any of his personal vendettas.
Soldier Boy and Homelander's choices also make sense when examined through a lens of character motivation. Homelander is the most powerful man in the world, a narcissist who wants to be adored by all. But he's also bereft of any sort of family at the beginning of the series, raised in a lab by Vought and Jonah Vogelbaum. He desperately hopes familial love will make him whole, and acts so desperately to make amends with Soldier Boy because he hopes the older supe can act as the father he never had.
In contrast, Soldier Boy chooses to fight Homelander because of the relationship he did have with his own father, one that taught him to hate weakness above anything else. He sees Homelander as weak because of his open display of emotion, and as such unworthy of any familial love. The Boys sets up the conflict between Butcher and the rest of The Boys by showing how they disagree on if or how the ends justify the means. It sets up conflict between everyone else by showing what they value most and then letting those motivations play out to their natural conclusion -- a fast-paced, uncontrolled blitz of creative violence.
All three seasons of The Boys are available to stream on Prime Video.