Harris is an FBI Supervisor Agent-in-Charge specializing in investigation of the DiMeo crime family with the FBI's Newark Organized Crime Division Task Force. While investigating the family, he develops a somewhat friendly rapport with several of its members, particularly Tony Soprano. Like Tony, Harris is a fan of the New York Mets. Recently returned to the United States after being assigned to counter-terrorism duty in Pakistan, where he caught a bad stomach parasite. Nevertheless, he frequents Satriale's pork store, apparently for the familiar food and company, but has also approached Christopher for information on terrorism-related organized crime from his criminal connections at the Port of New York and New Jersey. He is seen by Patsy Parisi staking out Moltisanti's rehabilitation centre. With Harris now focused on terrorism, he and Tony seem to develop a more genuine friendship. In the Season 6 episode "Kaisha", Harris appears at Satriale's to inform Tony that someone in his crew could be in danger, although he had no specific details.
Later on, Agent Harris and his partner, Agent Goddard, approached Tony at his home, requesting that Tony inform them should he come across any terror-related information in his line of work. Tony initially rejects the overture, but has a change of heart after suspecting that two Muslim former patrons of the Bada Bing, who had been paying Christopher Moltisanti for stolen credit card numbers, were involved in terrorist activity. Tony provides their names and a cell phone numbers to Agent Harris, who is appreciative. In return, Agent Harris promises to write a letter detailing Tony's assistance that will be placed in Tony's FBI file for a judge to consider in sentencing should Tony ever be convicted of a crime. Harris and Soprano seemed to have established a mutual respect at this point; Tony views anti-terrorism as an important issue and Harris appreciates that Tony's leadership is preferable to that of mobsters like Leotardo. He later tells Tony at Satriale's that an informer amongst Phil Leotardo's crew has told them that Tony is being targeted by the Lupertazzi family. Agent Harris meets with Tony Soprano, who offers him the name of the Muslim men's bank. In return, Harris tells Tony that Leotardo has been making calls from a pay phone in Oyster Bay, Long Island, information he apparently obtains from an agent with whom he is having an affair. When Agent Goddard later reports Leotardo's murder, Harris exults in the success of his ploy.
Upon hearing that Phil Leotardo was killed, Agent Harris jubilantly cries, "We're gonna win this thing!" This is a reference to former FBI supervisor R. Lindley DeVecchio, who said the same thing when he was told Lorenzo "Larry" Lampasi had been shot to death in front of his Brooklyn home. DeVecchio was later indicted for providing the Colombo family with information that led to four murders, much as Harris provides Tony with information leading to the death of Leotardo. Agent Harris' motivation may be personal. In an earlier Season 6 episode, Agent Harris tells Tony that he has never liked Phil Leotardo ever since Phil tried to set up a female agent for "a rape and beating." Late in Season 6 we learn that Agent Harris is either married to or more likely having an affair with a female FBI agent who indirectly appears to be the source of his info on Leotardo.