After failing to prise Ryan's location from Butcher earlier in The Boys season 3, Homelander turned his attention toward overtaking Vought instead, but rediscovering the value of family through Soldier Boy might inspire him to pursue Ryan even more feverishly as season 4 looms in the distance. This storyline provided the basis for The Boys season 3's daddy dilemma, as Homelander's DNA derived specifically from Stormfront, and their connection isn't quite so straightforward as "Father and son" (Stormfront is male in the comics).
The revelation that Soldier Boy is Homelander's father, and what this means for The Boys' future, is covered in The Boys season 3, episode 7. In exchange for the Boys' assistance, Soldier Boy agreed to fire his Compound-V-cancelling energy blast directly at Homelander's face, rendering the Seven leader mortal and allowing Butcher long-awaited revenge on his fated nemesis. "That's impossible" is Jensen Ackles' line after Soldier Boy bashes his brains into mush in The Boys season 3, episode 7.
From 1984 to The Boys' present day, Edgar's overarching goal has always been putting supes in the US military, and the future CEO might've deemed Soldier Boy ill-equipped for those purposes. In the closing moments of The Boys season 3, episode 7 "Here Comes A Candle To Light You To Bed" Homelander receives an unexpected phone call from Soldier Boy, who stunningly claims they're father and son. There's no way to tell if it's happy families or if Homelander will get 41 years of fatherly disapproval in one fell swoop.
Either Vogelbaum inseminated an unnamed woman volunteer with Soldier Boy's sample and they carried Homelander to term, or the scientist swiped a female supe's eggs just like he stole Soldier Boy's swimmers. The ever-shrewd Madelyn Stillwell probably joined the inner circle sooner or later because of her close relationship with Homelander. The Boys must face off against the Soldier Boy & Son in the final battle of the season after Billy Butcher's previous arrangement was null and void.
Billy Butcher's new best friend has been firmly on the warpath in The Boys season 3, carving through the ex- members of Payback who betrayed him. The only deep connection Vought's flag-clad imbeciles have in The Boys' comic books is their unfortunate tryst with Homelander. Stormfront seems to be the most obvious choice, partly because of the comic books, but also because it makes sense that Vought would combine their two strongest heroes if creating a perfect super- baby was the end goal. The idea of Stormfront being Homelander's mother is gross, but wouldn't you rather go to The Boys?
Considering Antony Starr is a little older than Jensen Ackles, The Boys season 3's father-son dynamic is a little off, visually speaking.
It's not something you'll find in The Boys' comic books, because they have sex in the source material. Vought doesn't know if Homelander will age normally, mature slowly, or remain in his physical prime indefinitely like Soldier Boy and Stormfront. Both were injected with Compound-V as adults, and the drug effectively froze them at those ages, but because Homelander possessed Compound-V from birth, his biology works a little differently. Jensen Ackles' hedonistic hero was either too high to ask questions or used to being poked and prodded by scientists, so he didn't think the ejaculation experimentation would herald the birth of his son.
The Homelander fetus spent a full 9-month term gestating despite being Vought's lab rat, because Soldier Boy gave a time frame of Fall 1980 to Spring 1981 from conception to birth.
In the past, The Boys have let audiences know that Payback was responsible for Soldier Boy's disappearance in 1984. Homelander will be inspired to play a more active role in his child's life regardless of whether the next bonding session with his dad is a hug-fest or a bloodbath. As it turns out, Soldier Boy's wild behavior was a liability, and that a lab child raised from birth would be more easily controlled. After Soldier Boy was captured by Russians, Homelander became the world's most powerful and popular supe.