Approximately two weeks after the hosts took over, Stubbs is on the beach at the edge of the park helping the PMC and the Delos Extraction Team with their rescue operation. He rescues Bernard from some soldiers, unaware of Bernard's true nature, and takes him to Delos Head of Security Karl Strand. Stubbs tries to defend Bernard when Strand accuses of him of failing as Head of Behavior for the hosts, but is quickly reminded by Strand that as leader of the security force Delos suffered the single greatest loss of life under him.
Later on he joins the security team in investigating the scene of the massacre, finding the dead body of Robert Ford in the process. While approaching a location where the hosts supposedly are, the team is startled to find the rotting host corpse of a Bengal Tiger from Park 6: Stubbs points out that they have never had hosts stray from their parks before. Continuing on, they discover an entire sea has emerged in the middle of the park, and floating in the water are the corpses of hundreds of hosts.
Stubbs joins the security team as they arrive in the underground, where they meet up with Charlotte Hale.
Some time after he was initially attacked by the Ghost Nation hosts at the start of the host uprising, Stubbs is at a camp of human hostages while being harrassed by Ehawee, when Grace is thrown next to him. He tells her about the protocol for guest evacuation, but she says she does not want to leave the park. After Grace breaks free from their captors, Stubbs is subdued and a knife is placed on his throat. The wielder, Akecheta, whispers in his ear (in English, whereas they had previously only spoke in Lakota), "You live only as long as the last person who remembers you." After a dramatic movement of the knife, Stubbs suddenly finds himself alone, but alive.
Stubbs arrives at the Mesa in time to meet Charlotte Hale, who brings in a struggling Peter Abernathy and retrieves a tablet to contact Delos. Stubbs reacts in disbelief that she is only now calling for an extraction team, but Charlotte explains that Delos would not send for help until Abernathy was safe. Stubbs helps Hale and some technicians restrain Abernathy in the Behavior Lab and Diagnostics area, but reacts with horror when they decide to nail him to the operating table.
Outside the Mesa, Stubbs meets with the extraction team, led by Coughlin, who refuses to cooperate with Stubbs, accusing him of letting the situation in the park occur.
In the present, Stubbs pulls Bernard aside and warns him that the Delos team is more interested in extracting their data than rescuing people and suggests they make their escape, to which Bernard agrees. On their way out, however, they are stopped by Strand, who thinks one of them has the key that motivated them to kill Theresa Cullen: Stubbs is surprised, as to his knowledge Cullen had died in the park. They are taken to a Remote Diagnostic Facility where Cullen was killed, and Strand threatens to kill Stubbs, thinking he must be the one that killed Cullen. Just as Bernard tries to stop Strand, they are interrupted by one of the soldiers finding a locked door. Entering it, they discover numerous Bernard hosts, revealing Bernard's true identity to everyone. Stubbs later watches as Bernard is tortured by Hale through simulated waterboarding, which he is clearly disturbed by. After Bernard's information is extracted, Stubbs joins the group heading for the Valley Beyond.
In the past, Stubbs informs Hale that the train has been deliberately crashed into the Mesa. Coughlin orders Stubbs to stay and protect Abernathy. Stubbs later hears the team sent to confront the hosts getting massacred, and upon seeing Hale order Roland to cut open Abernathy and copy over his control unit, demands to know what is in Abernathy's head. Hale ignores him.
The task eventually takes too long and Hale tells Roland to simply remove the control unit. Hearing the carnage going on nearby, Stubbs loses his patience and pulls a gun on Abernathy, once again demanding to know what is in Abernathy's head. Hale starts to explain he has an encryption key that they need, but they are interrupted by the arrival of Dolores and Teddy, who holds back Stubbs as Dolores confronts Hale. Stubbs listens in as the hosts destroy the Cradle and protests as he sees Dolores about to torture Hale, but they are momentarily distracted by Abernathy recognizing Dolores and Teddy leaving to deal with some nearby gunfire. Stubbs seizes the distraction and helps Hale escape into an elevator.
On-route to the Valley Beyond, Maling reports several human life signs nearby. Stubbs replies that they must be the remaining guests and requests boats and some soldiers to help rescue them, but Strand refuses as he is not there for the guests. Hale interrupts and grants Stubbs permission, though she adds that they should go on-foot. Stubbs leaves.
Later, Stubbs oversees the rescue and departure of the remaining guests, only to see Charlotte Hale (now revealed to the audience as Dolores since before Stubbs and Bernard met up with her in the Hub in "Virtù e Fortuna") approaching the line. He confronts her, noting he thought she was working on retrieving Delos's information, to which she replies she has business on the main land. Pausing for a moment, Stubbs cryptically tells her that he has been working at the park "for a very long time" and he does not really trust Hale or Delos because his loyalty has always been to Ford. Essentially, it has been his "core drive." He then leans in and emphasizes that, with Ford gone, his duty has always been to protect the hosts in the park, hinting that he knows more about her than he has been letting on. He then lets her through the security.