- "Another job well done by Agent James."
- ―The Carpals in the Coy-Wolves
James Aubrey is a junior FBI agent and the current field partner of Seeley Booth. Originally a desk jockey at the outset of his career, Aubrey's chance came when he became involved with Booth and the Jeffersonian's investigations into a massive conspiracy; upon siding with them, he eventually ingratiated himself with Booth and the team and in time became recognized as Booth's right hand man and a full-fledged member of the FBI's Jeffersonian liaison group. By The End in the End, Aubrey gets promoted to Supervisory Special Agent by the deputy director after turning down the same promotion in Los Angeles.
- "My father is Philip Aubrey. Maybe you've heard of him. He stole billions from his clients, so I know how this works. So you say that you don't have an account worth 4.6, because today the value might be 4.63 or 4.8. So, in your twisted little mind, you've told the truth. And if the account's in the name of some holding company, then you can honestly report that you don't have anything that belongs to Christopher Pelant and Associates. Now, you should know that I actually helped bring down my own father, Mr. Dunlop. So bringing you down will be a piece of cake. And as my friends here can attest, I love cake."
- ―Aubrey in The Next In The Last
Aubrey is witty, smart, and clever, although he can break down. He can be arrogant at times. He also gets easily excited and can be described as eccentric; for example, he finds it easier to remember a specific fact when he is distracted about something completely unrelated. Early in his career, he tended to focus more on the implications of certain cases before recognizing the human element, such as when he was enthusiastic about the potential of nailing a human trafficking ring before he saw the victims of the ring and realized the human element of the case. He likes children and is shown to be good with them as well.
Unlike Booth, James demonstrates a voracious appetite for learning the science behind their investigations though his ability to comprehend it is still limited. He is an avid history buff and, while dating Jessica Warren, got interested in listening to podcasts on a wide range of subjects.
Despite regularly eating his own body weight in food, he maintains an excellent physique. In The Lost Love in the Foreign Land, he told Booth that he has a blood sugar issue. Caroline refers to him as 'scrawny.' Jessica tried to motivate him to go on a "junk food cleanse" in The New Tricks in the Old Dogs, but he fell off the wagon after a day describing it as a sacrifice that a man should not have to make. His penchant for eating also gives him the ability to discern whether certain foods are artificial or organic simply based on the aftertaste.
- "Huh?! Come on! I'm, like, a Forensic Food-ologist!"
- ―The Flaw in the Saw
His father, Philip Aubrey, was a high-profile stock trader, but was arrested when James was 13 for running a Ponzi scheme. When released on bail, he ran away to Croatia while leaving James and his mother broke and on their own. He revealed that he had a hand in arresting his father in The Next in the Last.
In Season 10 Aubrey shows up as someone who Sweets trusts within the FBI. The deputy director of the FBI has Aubrey follow Booth around and make sure he stays out of trouble. Sweets immediately accepts him as a part of the investigation team, as do the rest following the death of the former as the season goes on. Booth does not trust Aubrey at first due to the loss of his best friend, Sweets. Aubrey stated that Sweets trusted him. He stated that Sweets trusted him and by treating him like crap, he was treating Sweets the same way. He is concerned of Booth, especially in relation to his gambling addiction.
- "Look, I know that what happened to you is messed up, and then what happened to Sweets. But remember that Sweets trusted me to work with you. So when you're treat me like crap, you're treating Sweets like crap too."
- ―The Purging of the Pundit
In Season 11 Aubrey becomes more or less a full member of the team. Like in the previous season, the duration of the season consists of the Junior Agent being used as comic relief. But the mid-season finale starts with a body being examined in the field by Hodgins, Cam, and a few other policemen when a bomb goes off from inside the corpse. The blast kills 4 police officers. Aubrey grabs Hodgins and pulls him out of the way, shielding him with his own body. The shot ends with Aubrey on top of Hodgins, a pool of blood growing underneath them. Hodgins is 'fine', and is released as soon as they reach the hospital. Hodgins said he saw them wheeling in his partner and that it didn't look good. He was in surgery for three hours, getting seven pieces of shrapnel taken from his upper torso. Bones was very worried he would die, voicing her concerns to Booth. Aubrey wakes up to find that Jessica Warren had already visited him 2 times. He later sneaks out of the hospital to get in on the case, and earns a lot of concerned shouting from Booth.
In The Last Shot at a Second Chance, Jessica Warren was almost hit by a car, but Aubrey pulls her away at the last second. Afterwards, they share a very passionate kiss on the sidewalk.
In The Tutor in the Tussle, Aubrey has to deal with the return of his father Philip and whether or not to turn him in. Philip claims that he has a new family and needs Aubrey's help. Aubrey chooses to turn Philip in, having him arrested by FBI agents at the Royal Diner. Aubrey tells his father to never take credit for how he turned out as Aubrey became a good man in spite of his father, not because of him. Booth reassures Aubrey that he did the right thing and reveals that he has uncovered that Philip's so-called family was just another con he was trying to pull on Aubrey. In The Radioactive Panthers in the Party, Booth allows Aubrey to take lead on a case which he is able to get a confession from. At the end, Booth reveals that Aubrey has been offered a job as a Supervisory Special Agent in Los Angeles and the case was a test to see if he could handle it as a result, Jessica Warren breaks up with him in The Day in the Life. In The End in the End, Aubrey aids Booth and Brennan in finally stopping Mark Kovac. Afterwards, Aubrey reveals to Booth and Caroline Julian that he has decided not to move to LA after all. Instead, the same position has opened up in the Washington, DC office and he has accepted it. Having broken up with Jessica, Aubrey apparently turns his attentions to Karen Delfs who brings him some comfort food that he shares with her.
- John Boyd, the actor who portrays Aubrey, was initially supposed to be a secondary character. However, with the departure of John Francis Daley, he was promoted to main character and received opening credits from The Lance to the Heart onward.
- John Boyd is the real-life son of Guy Boyd, the man who plays Philip Aubrey in "The Tutor in the Tussle," Aubrey's father.
- Aubrey is revealed to have extensive knowledge of the history of the FBI when he helps the gang terminate Glen Durant's shadow government.
- Aubrey is shown to have an intense dislike for the rich, even more than Booth. He also seems to have a hatred for the capitalist system at large. This is due to his father, a Wall Street banker and fraudster, building a Ponzi scheme, and then skipping bail after being arrested and leaving Aubrey and his mother alone and destitute. (The Money Maker on the Merry-Go-Round)
- He is shown to have a more-than-competent understanding of chemistry, which he took as a subject (perhaps at AP level).
- He can read music fluently and is well-versed on music theory and terminology.
- John Boyd is, to date, the Bones actor who was promoted the fastest to main character from supporting character, after appearing in only one episode.
- He minored in religion in college, and he's very well-versed in the Bible.
- In the episode The Puzzler In The Pit, Aubrey says he had a grandmother with dementia.
- Towards the beginning of Season 10 in The Geek in the Guck, James starts to take an interest in the "cute squint", Jessica Warren. The two develop a type friendship, and their feelings for each other are hinted to be more than just those of simple friendship on several occasions. James referred to the two as the "Brennan and Booth 2.0" (The Woman in the Whirlpool), although their positions as Booth and Brennan's associates makes them more like "Sweets and Daisy 2.0."
- He can play the guitar quite well, as shown in The Cowboy in the Contest.
- In The Geek in the Guck, it is revealed that he enjoys playing video games.
- In The Brother in the Basement, Aubrey revealed that his favorite cheap whiskey is Old Foglesong which, according to Caroline Julian, is the cheapest of the cheap whiskey. It was named after one of the co-producers of Bones, Keith Foglesong. *Aubrey stated that his favorite spice is cinnamon. He stated that he has it with his coffee at the FBI office in The Death in the Defense. *Aubrey said that his father's name was Phillip Aubrey in The Next in the Last, but Karen Delfs called him Benjamin Aubrey in The Fight in the Fixer.
- Aubrey is a fan of the Chicago Cubs (The Murder of the Meninist).
- Aubrey was part of an a cappella group back in college. In the 2001 National Collegiate A Cappella Championship, his team won 11th place for singing "Daisy Bell (Bicycle Built for Two)."
- Aubrey called himself a "Forensic Food-ologist" in The Flaw in the Saw. He has been shown in previous episodes, such as in The Price for the Past, that he can discern subtle differences in different foods with similar ingredients just by tasting them as well as determining whether something is all organic or filled with preservatives just by the aftertaste.
- He dislikes rats and spiders, describing anything that crawls as his kryptonite.
- He can easily recognize clothing textiles, such as gabardine pants on a victim.
- He is knowledgeable about the classics, such as Seneca's writings.
- Despite teasing the squints, he owns a book entitled "Forensics for Knuckleheads."