Danny Beck is a CIA agent and a former brother-in-arms to Booth.
He appears first time doing clean-up on U.S. soil, which would seem to violate the CIA's own protocols. Booth willingly lets him go, and Danny keeps the Agency from throwing roadblocks in the path of the team's investigation into Jonas Siedel. As the case is closed, Danny informs Booth that "we owe you one", deliberately side-stepping the issue of whether the "we" in question is the CIA.
Danny is much closer to the center of things when he resurfaces, as he was the handler for the victim, Sari Nazeri. Booth and Bones go to break the news to Sari's brother Aziz and find Danny already there. Sari had provided the Army with the means to target a terrorist leader in Afghanistan, Ibrahim, and in return Danny had arranged their immigration to the States. Sari felt that, although the price of being unable to return to her home was high, it was worth it to be able to encourage the independence and education of women from her homeland without fear of reprisal.
Danny and Sari became romantically involved, and Danny gave her his Higginson Special Forces knife for self-defense. Since Booth knew that the knife was "a part of Danny", having saved his life in Mosul, Danny becomes the prime suspect. His affair with Sari would ruin his career, if publicized, so Danny also has motive. He does, however, persuade Booth he genuinely loved the Afghani woman and did not murder her. Unfortunately, the corrupt guard who had facilitated Ibrahim's escape from a U.S. military compound was looking to support 'chatter' that Ibrahim survived the airstrike arranged by the U.S. Army and made possible by Sari, so he killed the woman in Ibrahim's style to make it seem as if he was still around.
Johannessen's guilt is proven conclusively by the Jeffersonian team (and Booth), but he cuts a deal with the Department of Justice to provide details on the whole of Ibrahim's network in return for the murder charge disappearing and $10 million. Danny and Booth are both appalled and frustrated by this, but Booth comes up with a way, once Johannessen has delivered on his end of the bargain, to balance the scales of justice. Johannessen's rehab (from the blast that led to Ibrahim's escape) is paid for by the Army, which makes him still subject to military justice (which does not fall under the DoJ), and so his actions constitute murder and treason before a court martial, actions which, when proven, will carry the death penalty. After the killer is taken away by MPs, Danny (implicitly) agrees to "remember who your friends are next time, OK?".