What is Phase 2 in Fallout? Explore the meaning of the protocol initiated by Steph, her marriage to Hank, and the ‘Sanitization’ of the surface in Season 3.
The Fallout Season 2 finale left viewers with more questions than answers. The final episode was structured in a very specific way, presenting a long series of twists designed to disorient the audience and open up countless possibilities for the already confirmed third season.
One of the biggest cliffhangers in Fallout Season 2 is undoubtedly the moment when Stephanie locks herself in her Overseer office inside Vault 32, puts on the Pip-Boy, and sends a message to the outside world, identifying herself as Hank’s wife and activating the mysterious “Phase 2.” In doing so, Steph takes the reins of humanity’s destiny, revealing a much darker nature than we ever imagined and triggering a series of events that are yet to be fully understood.
But what exactly is Phase 2? In this article, we explore the meaning of this protocol based on what we know from the video games and outline what we should expect in Fallout Season 3.
Hank, Steph, and the Work for the Enclave
The activation of Phase 2 in the Fallout Season 2 finale fits into a broader context where we discover more about the true roles of Hank and Steph. One of the biggest twists of the season finale was learning that Steph and Hank were married before entering the Vaults. Added to this is another decisive element revealed in the final episode: the end of the world in Fallout was not a decision made solely by Vault-Tec or Robert House, as the Ghoul’s suspicions often led him to believe. There is a higher level of management—the Enclave—and they are the ones pulling the strings of the world’s fate.
At the moment, we don’t know much about the specific individuals within the Enclave. However, knowing that years before Cooper entrusted the cold fusion diode to the President of the United States—and that the atomic apocalypse was ultimately triggered through the use of cold fusion—it is easy to imagine that the Enclave represents the legacy of the U.S. government. They are the ones responsible for the end of the world and remain dedicated to pulling the strings of humanity’s destiny.
Hank works for the Enclave. It was already clear that his job extended far beyond mere Vault management. Throughout the second season, we witness the series of “experiments” Hank carries out. Experimenting with humanity seems to be one of the Enclave’s primary goals, and they probably view Hank as one of their most active and effective employees. As Hank explains to Lucy just before wiping his own memory, the surface is supposed to be the “true experiment.” Everything suggests that this mysterious “Phase 2” is the next stage of this grand trial.
The fact that Steph was married to Hank before the war, combined with her communication with the outside regarding Phase 2, suggests that Steph has also always worked for the Enclave. She was likely the one managing the experimental phase inside the Vaults, which has now reached a terminal stage. After Chet exposes her in front of everyone, it becomes clear that managing the Vault is no longer possible for her. This leads to the activation of Phase 2, which carries much broader repercussions than one might expect for the Vault itself.
Phase 2 and the Sanitization of the Surface in Fallout
So Steph retrieves the black Pip-Boy hidden in Hank’s keepsake box and contacts the Enclave, identifying herself as “Hank MacLean’s wife” and requesting to “initiate Phase 2.”
Although the series has not yet explained the technical details, Phase 2 appears to be the culmination of the Enclave’s plan for total recolonization. If Phase 1 was the “Wait” (survival within the Vaults), Phase 2 is the “Sanitization.”
It is highly likely that this mysterious Phase 2 is closely linked to what Hank told Lucy regarding the surface experiment. From this perspective, the second stage of the experiment involves “cleaning” the surface of its current populations, which the Enclave views as literal parasites.
According to the most widespread theory, Phase 2 in Fallout is also strictly connected to the mysterious FEV (Forced Evolutionary Virus), engineered by the Enclave specifically to carry out the genocide of humanity. In the video game series, the FEV is used to create Super Mutants, who represent the Enclave’s ultimate army.
This is likely the war we can expect in Fallout Season 3, with the Enclave returning to actively manipulate the world’s fate by purging the surface. This also means we will likely see Enclave members emerging from their cryo capsules to reclaim the world.
If Steph is the one to trigger Phase 2—so closely connected to Hank’s work—it is plausible to think that Steph knew exactly what Hank was doing outside the Vault. We can assume that Steph and Hank were aligned on the details of what was planned for the future, and Hank had entrusted the burden of triggering this phase to Steph.
Reconnecting the Dots: Why Does Hank Wipe His Memory?
There is an extremely compelling aspect to the human experiments, the work for the Enclave, and Hank’s specific role. In the Season 2 finale, when Hank and Lucy are on the surface discussing the experiments, Hank is fully aware of the imminent arrival of Phase 2. He knows the moment has come; he likely gave precise instructions to Steph to trigger it at the right time, before leaving the vault. But Lucy is there, and Hank knows that his love for her represents a massive obstacle to the work he performs for the Enclave.
We must assume that Hank knows exactly what is about to happen: a new wave of wars and the genocide of the human race, all at the behest of the Enclave. Facing him is Lucy—the daughter he loves so dearly, a symbol of idealism and moral integrity. Hank is perfectly aware of the judgment Lucy would pass on him once his role in the world’s future becomes clear to her.
In the final scene of Fallout Season 2, Hank is anticipating the horror to come. He sees the wars on the horizon and Lucy’s future contempt for him. There is no way to prevent her from discovering his involvement in this grand, dark design. Therefore, Hank chooses to erase himself. By resetting his own memory and personality, he ensures that the man he was no longer exists.
The Hank who helped the Enclave implement its diabolical plan is gone. And so is the Hank who was Lucy’s father. In a single stroke, he wipes away every trace of his past and his actions, hoping Lucy will never discover how deep his involvement went—or, even if she does, so that he won’t have to face her judgment.
This final act is a sacrifice that testifies to both his total devotion to his work and the profound importance he places on his role as a father. These two dimensions could no longer coexist in the future that is arriving. His gentle touch on Lucy’s face, even after his memory is gone, symbolizes the “good” nature that remains hidden in his heart.
What to Expect in Fallout Season 3?
The activation of Phase 2 in Fallout shifts the conflict to a global scale. It is no longer a struggle between individuals, but between the surface resistance and an invisible corporate force that has waited 200 years to reclaim what it considers its own. With Hank’s mind erased, Steph Harper has officially become the true face of the Enclave threat, and we can expect an even more central role for her in the coming season.
Meanwhile, the Ghoul is headed to Colorado, where it appears he may finally find his wife and daughter. Fans of the games know that Colorado is home to the infamous Vault 0, which will likely play a pivotal role in the war of Season 3. We also have to understand the new role of Quintus, who declares himself “The Destroyer” in the post-credit scene, and how the mysterious Liberty Prime Alpha will enter the fray.
Everything has been left intentionally hanging. If you feel extremely confused at the end of Season 2, you are in good company. The Prime Video production has chosen to open a long series of plot lines that will develop in the next season, where we will finally get answers. It will take some patience: filming for Season 3 is set to begin in May 2026, and from that moment, it will just be a matter of counting down the weeks.
