In the episode "Inquisition", Sloan attempted to recruit Dr. Julian Bashir - the genetically-engineered chief medical officer of Deep Space 9 - into Section 31's ranks, staging an elaborate deception using a holodeck in an attempt to test Bashir's loyalties. In this scenario, Sloan posed as Deputy Director of Starfleet Internal Affairs, claiming that there was a security leak aboard Deep Space 9. Accusing Bashir of having been recruited as a mole by the Dominion during Bashir's incarceration at Internment Camp 371, Sloan claimed to have a son who was killed by the Dominion, and that he believed that his son's death was a direct result of information supplied to the Dominion by Bashir. Bashir eventually realized that he was being deceived, and Sloan was forced to terminate the program. Despite this, Sloan expressed to Bashir that he had passed the test, and Sloan was no longer in doubt of Bashir's loyalty. Sloan subsequently offered him a position within Section 31, citing his genetically-engineered background and fascination with spy stories. Bashir ultimately declined the invitation, stating that he did not believe it was proper for an organization such as Section 31 to have such power, acting autonomously and free of any oversight. Detailing his experience with Sloan to Captain Sisko, Bashir expressed his surprise that Starfleet would have such a department. In an attempt to further investigate Sloan and Section 31, Sisko ordered Bashir to accept Sloan's invitation to join the next time Sloan made contact with him.
Sloan returned the next year in the episode "Inter Arma Enim Silent Leges". He traveled to Deep Space 9 to give Bashir his first "assignment". Although Bashir had refused to join, Sloan claimed that he had been "accepted" into the organization and thus was needed to fulfill his "duties". Sloan goaded Bashir into joining the operation by appealing to Bashir's love of fictional spy dramas and intrigue, stating that he was a man of mystery made for the job he was about to assign him. He instructed him to perform observations of various members of the Romulan government during an upcoming Federation-Romulan conference on Romulus, and in particular Koval, the chairman of the Tal Shiar.
At the conference, Sloan posed as Wendell Greer, a representative from the Federation Department of Cartography. Through a complex series of events, Sloan convinced Bashir that he was planning to assassinate Chairman Koval. Sloan hoped that Bashir's sense of ethics would force him to try to alert the Romulans to Sloan's apparent threat. Bashir approached Senator Cretak, who agreed to break into Koval's personal database in an attempt to find evidence that would reveal Sloan's threat. Cretak was caught while trying to access the classified files and brought before the Continuing Committee, where she was censured for her improper and possibly treasonous behavior.
Ultimately, the entire operation was revealed to be a ruse aimed at getting Koval – a Section 31 mole – elevated to the Continuing Committee. In addition, Admiral William Ross was revealed to be involved in the operation, working alongside Sloan. At the end of the conference, Sloan thanked Bashir for his sense of ethics and for doing "the right thing", while at the same time pointing out that Section 31 existed precisely to protect people like Bashir.
Several months later, while investigating a cure for the morphogenic virus that had infected Odo along with all the Founders, Bashir came to the conclusion that the disease had been engineered by Section 31 as a way to attack the Founders and end the threat of the Dominion. Bashir and his friend Miles O'Brien devised an elaborate scheme to lure Sloan to the station with the hopes of forcing him to reveal the cure to the disease. Bashir informed Starfleet Medical that he had devised a cure to the virus, knowing that Section 31 would send an operative to destroy that information in order to prevent it from falling into the hands of the Dominion.
When Sloan boarded Deep Space 9, Bashir stunned him and attempted to use Romulan mind probes to extract the information regarding the cure from Sloan's mind. Ironically, Bashir and O'Brien, supported by Captain Benjamin Sisko, resorted to the same kind of morally questionable practices that they accused Sloan of. During the procedure, Sloan triggered a lethal implant in his brain, committing suicide to prevent Bashir from finding the cure to the morphogenic virus. Bashir managed to prolong Sloan's life, but the implant had scrambled the operative's neural pathways and brain death was inevitable within an hour. Desperate, Bashir and O'Brien used a neural interface to link their minds with Sloan's in a last-ditch attempt to discover the information. Sloan attempted to distract the intruders with images of his wife, Jessica, his family, and an alter ego who professed to want to reveal the information but somehow was prevented from doing so.
Sloan's alter ego thanked Bashir for having set him free like that, for having showed him that ideology is a poor substitute for kindness and decency. He was about to hand Bashir the solution to a cure for the disease when suddenly Sloan's other side emerged; the Section 31 operative and devoted Federation citizen. He shot the alter ego in an attempt to prevent the information from reaching Bashir and before they knew it, Bashir and O'Brien were finding themselves amidst the ethical battle that had ensued inside of Sloan's mind. After dragging them through a maze, Bashir was finally able to access the information he needed buried away inside a mental recreation of Sloan's office. But, Sloan had one last trap planned for Bashir: with the secret of the cure revealed, Sloan offered to share with Bashir all of his secrets – enough information to bring down Section 31 entirely. This was the one thing Sloan knew Bashir could not resist, and the doctor was nearly trapped in Sloan's mind as their time grew short. Fortunately, O'Brien convinced him to leave in time. Although the secret of the cure to the morphogenic virus had been revealed, Sloan took the rest of his secrets about Section 31 to the grave with him.