Season synopsis
Contains spoilers for this season and earlier seasons.
Season 9 begins with Booth and Brennan estranged after he abruptly withdrew his acceptance of her proposal. Pelant had threatened to kill five strangers if Booth married her, and Booth keeps that reason secret to protect them. Their colleagues take sides while Brennan tries to trust that Booth has a reason. After she speaks with Aldo, a former Army chaplain now working as a bartender, she tells Booth she still has faith in him and leaves the next proposal to him.
The danger from Pelant keeps the team’s personal lives close to its cases. When he returns and presents himself as the only person who can help Brennan identify a serial killer, she sees through his attempt to replace Booth. Pelant triggers an explosion, and Booth arrives; Brennan urges him to stop the threat, and Booth shoots Pelant dead. He then proposes again, explaining why he had refused her. Brennan accepts, and the two prepare to marry.
Their wedding is nearly derailed by a murder investigation, Max’s hidden cash and a church fire, but Angela moves the ceremony to a place associated with a memorable exchange from their early partnership. They marry with their Jeffersonian colleagues present. Later, Booth is being considered for a Berlin FBI post when a conspiracy blogger offers evidence linking the McNamara family to corruption inside the Bureau. The blogger is killed, and after Booth investigates the blackmail files, armed agents attack his home. Booth survives surgery, then is arrested for killing three FBI agents; Brennan is taken into custody too.