Special Agent Barrett's advancement within NCIS began when she accepted a position which was Special Agent in Charge of a team based in Rota, Spain. Agent Barrett was Director Shepard's second choice for the position. The position had previously been offered to Special Agent Anthony D. DiNozzo, who declined the promotion preferring to remain a part of the team headed by Leroy Jethro Gibbs. As a result, Agent Barrett took the position instead and stayed in Rota, Spain until she was transferred to Washington D.C due to budget cuts.
In "One Last Score", Tony and EJ showed a romantic interest in each other. They eventually began a dating relationship, which Gibbs disapproved of it; however, the two are still in a relationship.
Agent Barrett is the niece of the former Secretary of the Navy, and it is heavily hinted by Director Vance that her promotion over that of Gibbs during the hunt for Cobb was due to this familial relationship.
EJ was transferred back to Washington following a series of serial murders by Lieutenant Jonas Cobb, then known as the "Port to Port killer", due to his particular methodology of murdering each victim in a different port. She pursued Cobb across multiple countries and through multiple cities with her team, Special Agents Simon Cade and Gayne Levin. During this time, she comes into direct conflict with Gibbs, who objects to both her methods and her perceived inexperience, while developing a strong romantic relationship with DiNozzo.
Ultimately, EJ, her team, and the MCRT discover the real identity of the Port to Port killer as Lieutenant Jonas Cobb, who became murderous after being trained as an assassin by the CIA in a program created by Director of NCIS Leon Vance, approved by Secretary of the Navy Phillip Davenport, and taught by CIA Agent Trent Kort. EJ and her team are also tipped off by an anonymous woman, who emails them with information. They pursue the lead to try and find who the woman is, going into an old office building and searching for evidence.
Unfortunately, the witness is actually Cobb, who was laying a trap. He ambushes the group in the building while they are clearing a floor. Both Cade and Levin are critically injured, and EJ is captured by Cobb. Gibbs and DiNozzo arrive several minutes later, and discover the bodies of Cade and Levin. Gibbs pursues Cobb while DiNozzo stays with Cade, who is still barely alive; Levin has bled to death. Gibbs then discovers and frees EJ, who has been locked in the trunk of her car with plastic wrapped around her head.
Following their return to NCIS headquarters, EJ removes a microchip from Levin's wrist, which proves crucial in the future.
Ziva David is soon captured by Cobb, and the team, while investigating the area where she was captured, come across Cobb, who surrenders to them. While he is being escorted to lockup, he knocks one NCIS agent unconscious, takes Jimmy Palmer captive, and forces EJ to drive him out of NCIS using the autopsy van with the threat of killing Palmer.
It is revealed that Cobb's targeting of EJ is solely because of her relationship to SecNav, who he blames for what he has become. Gibbs, Vance, and Davenport pursue him back to the office building where he ambushed EJ's team before, and find him "training" three hooded figures, who are bound and being sprayed by freezing water. It is revealed that this building was where he was originally trained, and that the three people he is torturing are Trent Kort, whom he apparently captured earlier; Palmer; and EJ. When confronted, he attacks Davenport, but is shot to death before he can fire a shot.
Following the death of Cobb and the loss of both of the Agents under her command, EJ takes a sabbatical to consider where she wants to go with her life. She and DiNozzo apparently continue their relationship, while she gain Gibbs' respect, who offers a her a welcome back at any time.
Several months later, EJ is seen attempting to return the microchip, which apparently is capable of unlocking any electronically secured door, to Navy Captain Felix Wright, a member of a Special Operations team with callsign "Phantom Eight". This eventually ensnares her in the machinations of the team's commander, a Naval officer who is stealing the microchips (each of which are able to unlock all electronic doors) from deceased members of his team and attempting to sell them to international bidders. Her boyfriend, Tony DiNozzo, has also been secretly assigned to recover the microchips and eliminate the mole who has been stealing the chips, under orders from SecNav Jarvis and without the knowledge of anyone else.
Ultimately, Captain Wright is killed by a member of the Phantom Eight, known as "Casey Stratton". His microchip is removed by Stratton, who then begins targeting EJ in an attempt to steal the microchip she is in possession of. She makes contact with Tony at this time, and the two come under fire from Stratton. They flee to Washington, where they ask for Gibbs' help.
Special Agent Cade, the only other surviving member of EJ's original team from Rota, is brought into Washington soon after. Unknown to EJ, SecNav believed him to be the mole, and had ordered Tony to kill Cade. EJ, Tony, and Cade are all lured into a trap, after Cade returns to Washington, receiving text messages appearing to be from each other to meet in an alley at night. Tony attempts to arrest Cade, but the three discover that neither EJ nor Tony had sent the texts. Cade is then shot through the heart - EJ is shot in her ribs, below her left breast, and Tony is shot in the shoulder, though his Kevlar stops the bullet. Tony hits his head as he falls and receives a concussion - EJ manages to escape before the shooter, revealed to be Stratton, can kill her. Following her escape, she disappears - both NCIS and Stratton begin a search for her. Stratton has orders to kill her, while NCIS is attempting to locate and rescue her. She ends up going into hiding, coming up with an alias, until she ended up being tailed by an assassin. She then called a naval officer that she knew for help. The officer picked her up at the motel, only to end up ambushed by the assassin in question and shot at first before the bullet ended up in the officer's neck. The assassin then set up the scene of the death to make it seem as though he was killed in a car accident. She then went back to the motel briefly and then attempted to hitch a ride at a truck stop nearby. She was then found by NCIS who was investigating the officer's death. Afterwards, she and DiNozzo, due to her earlier leaving DiNozzo for dead, had some tense feelings for each other. She then identified the assassin, although by the time the NCIS team (barring DiNozzo) located him, the assassin was found dead by being stabbed and then thrown off a building. She and DiNozzo later occupied a safehouse in the mountains until Stratton is arrested. After he was arrested, she then went to her parents home, as Stratton's arrest now freed her to visit her family, after she had to evade contact with them for understandable reasons.
Based on how she acts in Two-Faced, EJ appears to a be a highly career-orientated agent, focused on advancement and securing favor with superior officers. She is friendly with her subordinate team from Rota. She is willing to flirt with suspects in order to trick them into divulging secrets, a technique that Gibbs wholeheartedly disapproves of. It appears that she believes in unconventional methods of persuasion and investigation - when confronted by Gibbs after an interrogation of a suspect, he tells her the "correct" way in which to interrogate; she responds with, "Maybe that's the old-school way to do it." She appears to be one of the few agents who either do not respect, or are not intimidated by Gibbs, a trait that DiNozzo disapproves of, saying that "...if you mess with the Great White [Gibbs], you'll get bitten." When pressed about joining an agency her uncle has command of, and thereby influencing her career, she claims she earned her place in NCIS but soon stops arguing, possibly showing that she knows she is given the fast-track for being related to the Secretary of the Navy. She is also quite caring and protective about people close to her, such as Levin and Cade, whom both died.