Has McQuaid been set up to take the fall for the Chicago bombing? Or was he really behind it?
The answer regarding his guilt or innocent in the bombing is answered in Covert Affairs Season 5 Episode 10.
Annie trusts her instincts and believes in Ryan's innocent in the bombing and assists him in the quest to uncover the truth. She has an idea of who may have set up Ryan and they pursue that lead.
In the end, Annie will find out whether her instinct was right about Ryan and her target. The episode ends with two people shot and only one surviving. Who will live and who will die?