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"The Hole in the Heart" is the penultimate episode of Bones' sixth season, and the third installment of the sniper story arc, an episode in which the Jeffersonian team finds one of their own in the cross-hairs of Broadsky's sniper.
Jacob Broadsky returns with his sights set on Booth. The murder of a young army scout leads the Jeffersonian team to not only piece together his murder, but also lead themselves straight to Broadsky.
The series of events leading to his capture finds Vincent Nigel Murray in the cross-hairs of a bullet meant for Booth, resulting in the interns tragic death.
The Jeffersonian team struggles with the loss while ramping up their efforts to put a stop to Broadsky once and for all. Using the evidence from the body of the dead army scout, Hodgins deduces that Broadsky must be hiding out somewhere near salt water, leading Booth to confront Broadsky on a shipping pier.
The standoff leads to Booth shooting Broadsky in the knee, bringing him into custody, much to the relief of the team.
The aftermath of Vincent's death weighed heavily on Booth and Brennan, resulting in a rather emotional moment between the two, which leaves the audience whether or not the two did the deed.
In the end, the Jeffersonian team pays homage to their fallen colleague by singing "Lime in the Coconut" as they load his body into a hearse and see him off on his journey to be buried back in England.