Tom finds the box with the gun, passports, and money. He questions Liz about it because he claims that he's never seen it before. He offers to go into the FBI to clear his name. The FBI believes he's working for Gina Zanetakos and that he killed the FSB defector. It appears he was set up. The money traced traced back to Red and the gun had Gina's fingerprint on it. Also, the man that he interviewed with is Red's right hand man.
The case was corporate terrorism. It involved a bomb made out of a car. The bomb was set up to go off at the Houston port to drive up business at the New Orleans port.
Liz believes that Red was involved in setting Tom up and breaks off their working relationship.