In a story that takes place shortly before Paul Moses' retirement, Eyes Only begins with Paul visiting his brother, Charles, who is engaged to be married. Charles tells Paul that he wants nothing to do with him because of his profession as a killer. After telling Paul, who was currently going under the alias of Bruno Frank to stay away from his family, Paul flies out to Vienna, Austria for a meeting with a man known as Mr. Kane.
Mr. Kane is upset because he had to cancel a meeting to be in Vienna to meet "Bruno Frank", and is displeased when Paul tells him he's retiring. Kane tells Paul that there is no getting out of their business, that there was no retirement and no gold watches. Paul pleads with Kane and Kane folds, telling him that there's a rare procedure in retiring, though, he couldn't just stop, but had to be rotated out gradually. He told Paul he'd put him on a temp job, probably as security and that he had to see a shrink every now and again before getting out.
Ten months pass, and Paul is working security detail for Carver Hampton, an African-American former Mayor who is in the process of making a bid for being the Democratic candidate for presidency of the United States. During a talk with Carver, Paul advises him that he was to be assassinated that very day and urges Carver to postpone his announcement due to how solid the lead on his assassination was. Carver declines, saying that it would destroy people's hope to postpone his speech.
While on their way to the podium a woman in the crowd calls out to Paul and tells him she has information on the possible assassination attempt. When he draws close, she whispers "red" in his ear. Hampton and his people were loading onto the elevator to go up to the conference, Paul was the last on, and just as the elevator doors closed Paul drew his gun and killed everyone on the lift, including Carver Hampton himself.
After escaping the elevator and into the sewers, Paul comes to, wondering what he'd just done. While trying to break into a store, he's stopped by a police officer who tells him the town is on lockdown. Paul notices the same woman from before in the police officer's car, gun in hand, prompting Paul to kill the police officer before engaging the woman herself. After subduing her, he demands that she tell him who she's on the job for or he's going to clock her out. She tells him she's about to clock out anyway, showing Paul a kill pill in her lips before swallowing it and dying.
Paul breaks into the store and tries to get in contact with Kane. After telling Kane what happened, Kane asks him if he knows where the safehouse in East Atlanta is and to meet him there in an hour. After Paul hangs up, he asks why Kane is already in town.
At the safehouse, Paul cleared most of the agents, killing them silently before anyone noticed while working his way toward the house to Kane. While closing in on Kane from the backyard, he's stopped by Sarti who kicks Paul through the kitchen door, startling Kane. The two struggle, but Paul eventually kills Sarti with a knife to the back of the neck.
With the safehouse cleared of agents, Paul begins asking questions. It turns out that Paul was conditioned to kill Carver by the shrink Kane made Paul go to. That the orders came from the highest authority, that it was for "Eyes-Only" men like him. Kane says that Carver was "a King and two Kennedeys rolled into one" and thus needed to be taken out. Paul tells Kane that after he kills him he's going to go to the police and confess, but Kane says that there's already a patsy, and if Paul breathes a word of this to anyone that he dies along with his family. If he stays silent, they'll set him up with a pension, a house, and then he can make nice with his brother and live out the rest of his days in peace.
Paul calls Kane a monster. Kane tells him that he's no monster, but Paul is.