It has been six months since Booth and Brennan quit their respective jobs with the FBI and the Jeffersonian. Brennan has given birth to her second baby and Booth now trains new FBI recruits. The Jeffersonian team uncover a body burned in a car and originally confirm it to be Booth's as his gun was found at the scene and after examining the remains. Brennan goes to the Jeffersonian to do her own confirmation, and uncovers evidence that it is not Booth's. Agent Aubrey is forced to work with Agent Miller from Internal Investigations and she dismisses Booth's disappearance and adds him to the suspect list for the murder. Brennan soon discovers the body is of Jared Booth, Seeley's brother. Aubrey and Miller visit Kevin O'Donnell, a close friend of Jared's, but he is not cooperative. The team discover that Booth and four others were tracking down a drug lord. The FBI search the house and find three men dead in the main office and the safe empty. They later confirm Booth was present at the scene as lots of his blood was found there. Caroline learns that Agent Miller has been keeping a secret from Aubrey, that her partner is also missing and Caroline advises Aubrey to investigate. Booth tends to his wounds and it is revealed he is working with Kevin and that they have the cash from the safe.
In a flashback, Booth, Kevin, and the others destroy the evidence and burn the van with Jared's body inside. Booth insists he must be the one to do it. In the present, Agent Miller admits to Aubrey and Caroline that her partner, Richard, who went missing had a printed list of undercover FBI agents. The team discover a severed finger of Richard's fiancée, Chloe, in his freezer, and that she is missing and was being held for ransom for the list. After recovering evidence, the team discover the bodies of Richard and Chloe. At the Jeffersonian, Dr. Benjamin Metzger, a digital forensic scientist for the FBI arrives. However, evidence points to Metzger being the one that killed Richard and Chloe to get the list. Brennan is able to get Booth's location from Metzger. At the warehouse, Booth continues to struggle with his wound as the gang waits to sell the list for lots of money. Kevin gets a text from Metzger that says Booth is FBI and that he must kill him or the deal is off. Kevin does not want to kill Booth, but when the other two men discover this, a fight ensues. Booth is able to take the two men out and escape the building. The SWAT team arrives and Booth is reunited with Brennan. He later recovers in the hospital. Meanwhile, Arastoo and Cam break-up as he wants to move on, since Brennan has returned to the Jeffersonian, displacing him, and that jobs he would take would require Cam to leave the Jeffersonian and he does not want her to resent him.
Booth and Brennan return to their respective jobs at the FBI and the Jeffersonian. They investigate the death of a man found in a fish farm whose organs had been harvested and sold on the black market. Booth readjusts to work back at the FBI, where Aubrey has taken over his office, and is frustrated that his brother's ashes are missing. Meanwhile, Hodgins encourages Angela to show off her photography work.
The team investigates the death of a man whose remains were destroyed by coywolves and learn that he was involved in a competitive fantasy football league, to which several of the suspects are linked. Brennan enlists the help of fellow forensic anthropologist Dr. Beth Mayer (Betty White), who makes several contributions to the case. Meanwhile, Brennan tells Booth that she plans on killing off the character based off him in her latest novel, much to his annoyance, and intern Dr. Oliver Wells reveals to Hodgins that he's dealing with erectile dysfunction and seeks advice.
In a crossover with Sleepy Hollow, the Jeffersonian team find a headless corpse in a church during Halloween and are assisted by FBI agent Abbie Mills (Nicole Beharie) and Ichabod Crane (Tom Mison). They discover the victim is 200 years old and is linked to their current murder investigation regarding a medical student. The crossover concludes in the season 3 episode of Sleepy Hollow, "Dead Men Tell No Tales", which features appearances by Brennan and Booth.
The death of a U.S. Senator leads Booth and Brennan to investigate Capitol Hill, with suspects including his wife and the majority whip (Brenda Strong). Meanwhile, Caroline has Aubrey do a background check on intern Jessica, stating it is due to the high-level nature of the case when it is really just to look out for Aubrey. Aubrey discovers things from her past, but they continue their relationship anyway. Also, Aubrey tells Booth about his political ambitions to be a Senator in ten years.
The death of an escape artist whose remains are found in the woods leads Booth and Brennan to investigate the Magic Palace, the place where the victim worked, and various suspects within the magic community. Meanwhile, Sebastian Kohl returns to work with Angela on her photography and he later asks out Cam, but she isn't sure if she's ready for a relationship after her break-up with Arastoo.
The team investigate the death of a political journalist who published documents exposing corruption in the NSA. The killer is revealed to be the journalist's source for the documents who is also arrested for treason. Meanwhile, Booth's son Parker returns from London, and the Jeffersonian team celebrate Thanksgiving together.
Booth and Brennan go undercover as Buck and Wanda at a role-playing Old West-style shooting competition. While trying to catch a killer, they also go against one another in the shooting competitions. Meanwhile, Cam continues her relationship with Sebastian and Hodgins reveals to Angela that he's not ready for more children and is happy with the family he has.
The body of a police officer rigged with a bomb detonates at a crime scene, killing several police officers and significantly injuring both Aubrey and Hodgins. While Hodgins seemingly recuperates quickly, Aubrey is in more critical condition, requiring surgery. Booth is joined by behavioral analyst Karen Delfs who assists with the case and Arastoo returns to the Jeffersonian to help as well after hearing what happened. After solving the case, Arastoo confesses to Cam that he still loves her and Hodgins collapses in the lab. At the hospital, the team is informed that Hodgins is paralyzed due to the trauma he suffered from the bomb explosion.
Eight weeks after the bomb attack, Hodgins returns to work in a wheelchair, eager to get back to work. Despite his helpfulness with the case, Cam decides to send him home so it does not interfere with his recovery. However, she later reconsiders her decision and lets him return to work. Hodgins later receives a call from his doctor telling him he will probably never walk again and hides this from Angela. Brennan and Booth investigate the death of a public defender who had multiple prior clients with motives to kill her.
The team investigate the death of a man who was the founder of a men's rights organization. Brennan assaults a suspect, the organization's co-founder, after he makes misogynist comments to her. Hodgins' bitter attitude towards his paralysis causes a strain on the working environment in the lab and with his relationship with Angela.
The dead body of a social worker in a park reveals clues suggesting that the killer lived with the body for months before dumping it, and the discovery of a similar set of remains confirms it's a serial killer who uses the corpses as marionettes. Booth and Aubrey consult behavioral analyst Karen Delfs for clues; and Cam rethinks her love life when Arastoo comes back to the lab.
A female felon is found during a mudslide and Booth discovers that one of the suspects is someone he met while in prison. Brennan attends a hearing after punching a suspect (from "The Murder of the Meninist") and receives six months of probation with Booth as her probation officer. Meanwhile, Hodgins and Angela take a step in repairing their marriage; and Aubrey and Jessica continue their relationship.
When a body is found in the Potomac, the team discovers that the victim is both a private investigator and a fixer, making the suspect pool much larger. Hodgins is returning to his old self, but Angela thinks he is trying too hard and Aubrey is surprised when Karen Delfs suddenly asks him out. Brennan makes a bet with Oliver Wells when Christine is suspected of cheating on her report card. Later, Aubrey finds out that his father is back and has started an investigation into his own son.
When a male singer is found in a rat lab, Booth looks at two rival A Cappella groups for suspects. Brennan gets a new intern, but is irritated after the intern makes numerous mistakes, while Hodgins signs up for experimental surgery in an effort to walk again. After the case is solved, the team learns that Aubrey was also a singer in college. This episode features Kirstin Maldonado, Mitch Grassi, and Scott Hoying of Pentatonix, as well as singers Sam Tsui and Jordan Fisher.
A body found in the woods is identified as a Secret Service agent, which leads everyone to wonder if the murder was personal or an attempt to target the President. Aubrey is given a new partner when the Secret Service prevent Booth's involvement due to his relation to John Wilkes Booth. Fisher returns to lead the forensic side when Brennan is stuck at home with a cold.
A documentary crew follows the team around as they solve the murder of a man found in a landfill after a decade. Meanwhile, Arastoo tries to hide his feelings for Cam from the cameras, but Cam confesses her love and proposes to him, which he accepts.
Booth and Brennan are in the middle of spring cleaning when the decapitated body of a hockey player is found in the Anacostia River. Meanwhile, Oliver and Hodgins get competitive when Oliver beats Hodgins in a video game. Later, Booth settles an old score with a goalie against whom he played in high school.
The frozen body of billionaire explorer Henry Charles is brought to the Jeffersonian and the team is surprised when they discover Clark Edison was part of his last expedition 15 years ago and dismayed when he later becomes a suspect. Cam's sister Felicia returns to plan most of Cam's wedding and Cam struggles to keep quiet about her own wants to prevent any arguments.
A French inspector works with the team as they investigate a body found at a glass recycling plant with a diamond in its jaw. Meanwhile, Hodgins continues his physical therapy and has a breakthrough when he unknowingly knocks over objects in lab due to a muscle spasm in his leg. Booth is diagnosed with a temporary eye condition and needs glasses.
In the Season 11 finale, the search for the Puppeteer, a serial killer who turns his victims into marionettes, continues, but Brennan can't shake her guilt of failing to catch the perpetrator due to her brief period of retirement.