Cipher is easily one of the most mysterious characters in The Boys universe, but some intriguing developments surrounding the Gen V character have left enough room for theories surrounding who he is and what he wants.

Gen V season 2 has perfectly raised the stakes for its young superpowered characters by introducing a whole new supe villain, Cipher. In Gen V season 2’s opening episodes, Cipher only came off as another overambitious Goldolkin University dean who wished to fulfill his supe supremacist agenda.

However, as season 2 has progressed, it has become evident that there is more to him than meets the eye. He is not only extremely overpowered but also seems to want to achieve something far more than a supe-dominant world. Cipher’s history also connects him to Marie’s past, which leaves a lot of room for speculation surrounding what his motives truly are.

Cipher Is Not Actually A Villain

Gen V season 2 has been trying to portray Cipher as a villain since episode 1, but some things about him just do not line up with that image. Since the beginning, he has been trying to encourage Marie to reach her true potential as a supe and even told her she could become stronger than Homelander.

If he only cared about creating a world dominated by supes, why would he even compare Marie with the strongest supe instead of embracing Homelander for who he is? He even avoids responding to Marie when she asks him if Vought or Homelander would be okay with him trying to create someone so strong.

Every time Cipher catches the young supes spying on him and trying to expose him, he seems more disappointed by their underwhelming efforts than by their intentions. This, too, suggests that he might genuinely care about their well-being and is seemingly trying to help them.

Cipher Is A Natural Mutant & Wants To Create More Supes Like Himself

Gen V season 2’s episode 4 surprisingly reveals that no Compound V flows through Cipher’s blood. This initially makes Marie and her friends believe he is not a supe, but he later proves them wrong by mind-controlling Jordan. Owing to this, it is hard not to believe that Cipher might actually be one of the few or the only “natural supe.”

Most or all supes in The Boys‘ universe, including Homelander, have Compound V flowing through their bodies. They acquired their powers through Vought’s experiments and were not born with them. Ryan is perhaps one of the few exceptions to this. The problem with most Compound V-fueled supes is that they often have limitations or experience major side effects.

For instance, both Homelander and Soldier Boy show mental instability, while supes like A-Train have heart issues. Cipher, in contrast, might be a natural supe with no Compound V side effects because he was born with his powers. He seemingly hopes that after Marie learns to control her blood-manipulation powers, she will eventually be able to help him create more natural and pure supes like him.

His desire to create a more pure superpowered human race would also explain his past Nazi connections.

Cipher Is Secretly Working For Stan Edgar

Since Homelander has been growing from strength to strength both politically and socially, figures like Stan Edgar might have realized that it is time to end his reign. Seeing how several young supes have the potential to beat him, Edgar must have hired Cipher to help supes unlock their true capabilities.

If this holds true, Project Odessa likely involves the creation of a prefect Homelander replacement who can eventually restore balance to Vought’s power structure. This would align with The Boys‘ comics, where a Homelander clone, who dresses up as Black Noir, is asked to kill Homelander when the red-caped supe grows increasingly unhinged.

Cipher Killed Andre

Gen V has already established that Cipher has the ability to fully mind control other supes. Cipher also previously told Marie that he has been watching a lot of them, suggesting that he has had his eyes set on them since the battle of Godolkin from Gen V season 1’s ending.

Since Cipher’s goal has been to gauge the potential of younger supes, it seems possible that he started going in and out of Marie and her friends’ minds when they were imprisoned after the Godolkin battle. He was likely impressed by their resistance against other supes and was trying to understand who among them was the strongest.

He seemingly pushed Andre to his absolute limits to either test his powers or intentionally kill him before moving his focus to Marie. Otherwise, it makes no sense for Andre to push his powers to a point where he dies, especially after he knew how the same abilities harmed his father.

Cipher Is Nothing More Than A “Meat Puppet” For Thomas Godolkin

Gen V season 2 begins with a sequence in which Thomas Godolkin collapses to the ground in a burning lab after failing to stop a group of fellow scientists from experimenting with an early version of Compound V. In season 2’s episode 4, Cate finds a burnt man in a hyperbaric chamber in Cipher’s home whose vital signs monitor reveals he is still alive.

Connecting the dots, it is hard not to believe the man in Cipher’s home is Thomas Godolkin. A popular theory suggests that Cipher, as we physically know him, is nothing but a “meat puppet” for Thomas Godolkin. Thomas Godolkin is the one with mind-controlling powers and is merely hosting Cipher’s body.

The Hamish Linklater character was a normal human before Godolkin took control over his body, which could explain why he has no Compound V in his blood. Godolkin’s body was damaged beyond repair during the lab fire, but his supe powers are so strong that he can even mind control others through his host, explaining how Cipher controls Jordan.

According to this Gen V season 2 theory, Thomas has been trying to train Marie through Cipher to become the strongest supe in the world because he hopes to host her body next. Since he sees humans and supes as mere meat puppets, it would explain why Cipher tells Marie that people are nothing but bags of blood.