If you're reading this, then you've managed to watch through season 1 of Amazon Prime Video's The Boys, all the way up to that "WTF?" cliffhanger ending. The final scenes of The Boys may hit too hard and fast for some fans to really make sense of all the major reveals, and how they redefine the events of the series. Not to worry: we've got the explanation you need.
It goes without saying that MAJOR SPOILERS for The Boys are about to follow, so don't read any further unless you've gotten to the ending!
The final episode of The Boys sees Butcher's (Karl Urban) team (the titular "Boys") falling apart, as Vought International and their super team The Seven finally uncover who Billy Butcher and his cohorts are, and start to close in on them. Before long, half the team is locked up in Vought's facility, but in the case of Hughie Campbell (Jack Quaid) it turns out to be a Trojan Horse play: Hughie manages to get the rest of the captured team (Frenchie, Alonso, Kimiko) out, and with a little help from his lover Annie/Starlight, Hughie even gets justice against his nemesis, the speedster A-Train (Jessie Usher).
While The Boys manage to escape and go on the run to fight another day, Billy Butcher puts himself on a much darker suicide mission: Infiltrating Vought executive Madelyn Stillwell's (Elisabeth Shue) home, and turning her into a human bomb to leverage against the all-powerful Homelander. Billy's plan is sound, except for one glaring detail: it's all based on a pack of lies.
What we learn in The Boys finale is that the roots of conflict between Butcher and Homelander are all based on misconception. Butcher believed that eight years ago Homelander raped his wife Becca (Shantel VanSanten), a Vought PR exec, causing her to have a mental breakdown, leading Bill to believe she either ran away or got killed to cover the Homelander’s shining image. What we come to learn, however, is that Becca and Homelander's tryst was entirely (mostly?) consensual, and that Becca's mental anguish thereafter was because she'd actually been impregnated by the superhero. It's never explicitly stated why she left Bill, but presumably, carrying the baby of Homelander would be a big enough threat to motivate her into a sort of witness protection restart.
Meanwhile, Homelander never knew about his baby with Becca, as Madelyn worked with pioneer genetic engineer Dr. Jonah Vegelbaum (John Doman) to cover up Becca's pregnancy, as well as the fact that Homelander (who was supposed to be a sterile genetically-engineered superman) can produce viable offspring. Becca successfully gave birth to her and Homelander's son, while Madelyn and Dr. Vegelbaum created the false "secret" of Becca having a nightmarish delivery and the super-baby dying in labor, to throw off anyone who came asking questions. Unfortunately, by the time Homelander shows up at Madelyn's home to confront Butcher, the psychotic hero has already tortured Dr. Vegelbaum to death to learn the truth about his son. So, while Butcher thinks he has leverage, Homelander instead him brutally murders Madelyn, leaving Butcher with the suicide option of blowing himself, Homelander (and presumably Madelyn's infant son) all up.
...Which proves easier said to done, when a superman is in the room. Homelander saves himself and Butcher from the explosion (no word on the baby yet), and by the time Butcher wakes up from the concussive blast, he's in small town USA being confronted with a horrible realization: His wife has been alive all this time, and she's been raising a super son in secret. Given how violently and brutally Butcher has been in his quest to kill all supers and get revenge for his wife, it goes without saying that this twist ending is going to be a major mind-f*ck for Mr. Butcher!
The Boys season 2 has already been announced. Season 1 is now streaming on Amazon Prime Video.