I've got an insane theory ..

Don't tl;dr and then say it's wrong.

It all starts with s2e11 the groovy gang/Venturestein episode. As we know this is the episode the boys discover their own clones.

And before I get into all the "here's why and where's". Let me just outright state where I'm going with this.

My theory surrounds the idea that Doc found out he was a clone many years ago. After coming to grips with it all, it occurs to him that he would have been a much better father than Jonas ever was to him. So with this sudden realization of superiority over his own father, he sets out to prove his theory by raising himself, Dean. But originally named him Dave. He had a lonely childhood, likely wishing he had a sibling better brother than The Monarch, when he was around that is. One who could have protected him maybe, but never out shined him.

And How does Doc make that happen? He clones his current bodyguard, Myra of course. Who would have been named Dawn at first.

At some point the kids get killed. Perhaps Myra killed them first idk. Which is how she wound up in the crazy house. Actual evidence of her being a baby killer.

But after that first death Doc found it hard to deal so he decided to clone them back to life. He already did it with Myra once and used an old slug of himself he can just do it again. But during the slug stage something went wrong with Dawn's chromosomes and they didn't fully form. Leaving an incomplete X to become a Y, creating a boy. By the time Doc realized this it was too far gone to fix. Thinking it was probably a happy accident now that the companion he created for Dean, can now be a twin brother who perheaps could end up a bodyguard for his future self/Dave/Dean. With this in mind and the kids Death likely being public. Doc changes their names from Dave and Dawn to Dean and Hank. And this time he made sure there were backups. Which is why the OSI never caught on about his illegal cloning operations. The boys always seamlessly come right back. Nobody questions it except 21 and 24. Who have killed them.

Now back to s2e11: At the very start of this ep Doc is creating Venturestein. After his success everyone crowds around looking at his creation. One of the boys mentions something like Doc was his father, seconds later Venturestein calls Doc "Father" flattered, Doc laughs "oh no please don't THINK of me as you're father. I get enough of that noise from these two." referring to the boys. I don't generally get caught up in words. But Doc and Jackson pick them all so carefully. Why didn't Doc say don't CALL me that. . Instead he said THINK. It implies they think he's their father, but he's actually not. And potentially regrets it. s1e2 "it all started with a moment of passion and it'll end that way .." doesn't have to mean sex. Doc is passionate about science and passionate about being better than his father. Even though he fails miserably at both.

Now back to s2e11, during this episode the groovy gang turns up and Val goes on about her hate for men. But with in her rant is a huge clue. She talks about men being incomplete females referencing their Y chromosomes. Shortly after that the groovy gang chases the boys into the lab where all of their clones are.

I find it hard to believe as coincidence that we're educated on the basic science of chromosomes moments before the boys find themselves. It was a hint at something being awry. Also I'd like to point out s2e10 is the episode we're introduced to Myra. Just 1 episode before.

S4e11: This episode centers about #2's being kidnapped. But on the side there is Doc, just waiting to be kidnapped with them. But it was never happening so Hank and Hatred kidnap him to save his ego. During this time Doc hears Hank and Hatred complain about Dean saying they're gonna kill him, figuratively. Doc unaware of this says in a panic "he'll pay whatever they want." To their surprise he acted like a Dad. So Hank, wanting in on some of that love and affection, mentions they have Hank too! To which Doc replies "oh, well if you're gonna kill anyone, kill Hank." Complete and utter lack of giving a shit about him, why? He's not his flesh and blood. Just a ward he's been raising in good faith he'll protect his son, who is really himself. And Doc only cares about himself. Lucky for Dean.

Hank later asks why he doesn't care about Hank, Doc goes on to say, Dean should have been Rusty Venture (implying he could have been if his slug was pulled instead.) because he believes all this crap. But he then goes on to say how much of himself he sees in Hank and he wants to apologies to him for it but there's no escaping it now. He's a Venture. Why apologies if it was down to genetics? I think he's sorry because he created him, and mistakenly in his own image, by coddling Dean and ignoring Hank as Jonas ignored him. And even if he found out that he was a clone of Myra, there is nothing Hank can do to escape it, he's a venture. This may all be a prelude to Hank arching Dean.