Paul Shepherdson (Richard Gere) is Cassius. (This is revealed really early.) One of the Cassius Seven group killed his wife and child so he went about murdering to get revenge and basically stayed in the US as an agent investigating the Cassius group as a cover while he killed people and specifically the Cassius group members.
Ben Geary (Topher Grace), as it turns out, is also a Russian double agent, brought from Russia as a baby, trained by his parents, became a member of the FBI and then activated a year before by the Russians. He's the one who arranged the original murder that Shepherdson gets called out of retirement to investigate in order to draw him out (since he went off on his own after the murder of his family) so that they can pin some murders on him and help some new Russian bad guys get into the country without getting caught.
Paul goes after one of the last remaining Cassius Seven guys, the one who killed his family, and Ben goes after Paul. Ben is supposed to expose Paul as Cassius after killing him and then return to Moscow. They have a little conversation before pursuing the last of the Cassius Seven guys, Paul tells Ben he knows he's a Russian double agent, knows what his assignment is (to kill Cassius) and Ben basically tells him they'll pin the whole thing on the other guy instead of following his orders.
Ultimately, though, Paul and the Cassius Seven guy are both killed by Ben. Ben reveals Paul's watch, on his dead body, has a wire used for slitting throats in the Cassius manner thus exposing him for the director to see and making himself a hero.
Ben then drives home, sits outside for a minute, and then goes inside, leading us to believe he too is picking family over country.