In 2023, Holly notified him of an assignment to hunt the replicant Eve. He accepted and his search for her led him to the Chinatown district, meeting Eve at a club. However, he was ambushed and knocked unconscious. When he came to, he filled in Gaff on the case and gathered evidence from the scene, including a memory cube and recordings of the replicants mentioning "Night Owl" and "Nakayama."
He returned to the LAPD headquarters and discussed the rumored mole in the department with his colleagues Sims, Taverner, and Mackey. He gave Mackey the memory cube he found and went to Captain Holden's office, accepting the job of finding Kano Nakayama, a founding partner of the Tyrell Corporation who went missing two days prior.
Harper was sent to the Tyrell headquarters and was informed by Lilith Tyrell's assistant, Santiago, of Nakayama's secret apartment. He then spoke with Lilith, who was concerned that the replicants knew of "Night Owl," a concept that she said would change the future for replicants.
He went to Nakayama's penthouse and used his multitool's Esper function to re-create the scene of Nakayama being kidnapped by the Replicant Underground Resistance and gathered evidence, including a forgery of his Blade Runner badge, a chess piece inscribed with Isaiah 34:14, Nakayama's neural kernel, and an eyeball. He also learned that Night Owl was the codename for a pathogen that was tested on Keith Arem, a Nexus-6 replicant that died six minutes later.
Harper was ordered by Gaff to run a Voight-Kampff test on Lazarus, a prisoner that had been apprehended in Chinatown. The test determined he was a replicant, but Harper let him go, believing he would lead them to Nakayama.
Lazarus was tracked to a rooftop where Nakayama was held captive. Harper managed to subdue Lazarus, but Nakayama was killed by Eve.
Holden ordered Harper back to his office, but was first stopped by Gaff, who advised that he tell the truth about his investigation. Holden arrived and asked Harper about Lilith, who had gone missing, with Santiago claiming Harper had requested a meeting with her. Because Harper withheld the forged badge, Holden suspected him of being the department's mole and subjected him to a Voight-Kampff test. During the test, Gaff entered, informing Holden that Lilith was found at her office. Holden told Harper to go home and return first thing the next day to take another Voight-Kampff test. He then received an encrypted message from Eve, who requested his presence at her "fourth and final birthday party."
He went to Eve, finding that the group had Lilith held captive and had used Nakayama's assistance to remove her eyes and place them in a replicant of her to use for their cause. Eve tells Harper he is a replicant and urged him to join their cause by killing Lilith.
If Harper shot Lilith, he was told by Eve to protect the replicant Lilith and to destroy Night Owl. Eve's lifespan then expired and she died. On his way back to his spinner, Holly revealed herself as the mole, commending Harper for his actions.
He went to the Tyrell headquarters, where Holden had confronted Lilith. When Holden learned of Harper's deception, several other Blade Runners reached the premises and engaged in a gunfight with Harper, who managed to kill them and Holden. Lilith then sent him away with Night Owl.
Now a member of the Resistance, they offered him the job of smuggling a "very special" child out of the city.
If Harper shot Eve, Lilith begged him to stop the replicant Lilith. On his way back to his spinner, he was attacked by the replicants Epiphany and Jones. After Harper retired them, Holly revealed herself as the mole, expressing her disappointment in his actions.
Harper triggered Holly's shutdown mechanism and made his way to the Tyrell headquarters, where Holden had confronted Lilith. Harper then exposed Lilith as a replicant and she attacked Holden, prompting Harper to shoot her. Holden commended him for saving his life and helping the LAPD retrieve Night Owl.