There’s no doubt that the world of The Boys likes to keep us on our toes. So, it wasn’t really that surprising to find out that Cipher is a Supe, but one of a different variety in Gen V season 2, episode 4. This opens the door for a major connection to Thomas Godolkin.
Caution: This post contains SPOILERS for Gen V season 2, episode 4.
While training with Cipher, Marie noticed that he had no V in his blood. This told her that he was human, but it didn’t take long for that theory to be proven false. Cipher is a hugely powerful but unique Supe, and he is a bigger threat now than ever before.
He also knows a lot about Thomas Godolkin. It leads to a major theory about who he could be, and how he could be linked to God U.

Is Cipher the son of Thomas Godolkin?
All we know about Thomas Godolkin is that he was the founder of Godolkin University. It turns out that there was a much bigger reason behind the university, and that was Project Odessa, to find the most powerful Supe the world has ever seen: much more powerful than Homelander.
They seem to have found that in Marie, but she needs to be trained. Cipher is the one doing the training, but that has led to a few secrets coming out.
It could be possible that Cipher is the son of Thomas Godolkin. I wouldn’t put it past a scientist to run some tests on people close to him. Considering there was a whole project running tests on babies, it makes sense that he would want his own child to be part of that. Considering Cipher was around to deliver Marie, it would suggest that Cipher was the first of the babies to ever go through it, and maybe he was the only success until Marie.

Cipher could be Godolkin in Gen V
But let’s look at another theory. Marie’s aunt said that Cipher’s name was Dr. Gold. Considering his Supe name Cipher, it wouldn’t be surprising that Gold is taken from Godolkin a little. It’s not like he could call himself Dr. God for short, is it?
We didn’t see Thomas Godolkin die in the Gen V season 2 premiere, which hints that he will be back in some way. It wouldn’t be the first time that a Supe has lived for decades and still looked young. Just look at Stormfront and Soldier Boy! With Cipher clearly being a different type of Supe as well, it would certainly be plausible for it to be Thomas Godolkin, who is still young but looks different due to the injuries at work.
My only issue here is that there’s the burned man in the hyperbaric chamber, which I would assume was Thomas Godolkin. What are the chances that Cipher is Odessa, but that he needs Marie to help heal his father, Thomas Godolkin? I think the idea of Cipher being Godolkin is too on the nose and obvious, and The Boys doesn't tend to do obvious, so the son of Godolkin makes more sense.
Gen V airs on Wednesdays on Prime Video?