Thomas Rhumor discovers a four-leaf clover inside his morning newspaper, then commits suicide.
The same day, Will Travers, an intelligence analyst at the American Policy Institute (API), spots related crossword puzzle answers in multiple newspapers involving the government and a four-leaf clover. Will notifies his boss, David Hadas, who then notifies his boss, Kale Ingram. The next morning, David dies in a train crash.
Will begins to investigate David’s death with the help of Ed Bancroft, a retired API analyst and David’s former friend. Meanwhile, API director Truxton Spangler meets with a group of men and tells them that Rhumor's demise puts them "back on track."
Will succeeds David as the leader of an API analyst team that includes Miles Fiedler, Grant Test, newcomer Tanya MacGaffin and assistant Maggie Young. The team is assigned to analyze a photo of Yuri Popovich (a Russian arms dealer) and two others later identified as banker George Boeck and one Tanaz Sahar, who runs a Middle Eastern foundation. That assignment is briefly shelved so the team can assess intelligence related to a proposed missile strike targeting a terrorist named Kateb.
Tom's widow Katherine Rhumor is surprised to learn her inheritance includes an Upper East Side townhouse, from which Tom’s friend James Wheeler later surreptitiously removes a photo of seven young men at the beach.
Will's research into David’s death leads him to Donald Bloom, a former covert agent whom Will later sees having lunch with Kale. Will learns that Bloom frequently visits Houston, and also discovers that an API white paper entitled "The Houston Problem" is missing from API’s library. (Spangler, in possession of the document, shreds it.)
Kale offers help for Will’s investigation and steers him away from Bloom and towards Edward Roy, whom Will traces to a security company that is a subsidiary of Atlas MacDowell.
Katherine investigates her husband’s suicide; her research leads her to Alice Bradley, the widow of Gerald Bradley, the suicide whom Tom succeeded on the Atlas MacDowell board. Alice reveals a four-leaf clover found near her husband's dead body.
During an FBI lockdown to investigate a suspected leak within API, Will notices an Atlas MacDowell paperweight in Spangler's office. Will later sneaks back into Spangler’s office and steals a surveillance CD, on which he hears David telling Ed, "They used your crossword code."
The CIA whisks Tanya and Miles to a classified location to evaluate information obtained during an interrogation of a suspected associate of Kateb. Miles determines the CIA is trying to link Tanaz and Kateb.
Spangler, Wheeler, and another man gather to discuss world trouble spots. Wheeler assures that Katherine is "not a problem.” He later draws a four-leaf clover on the back of the beach photo and mails it to her.
Will visits the office space housing Atlas MacDowell. He also finds an Atlas phone list that includes Truxton Spangler’s name.
Unnerved by the surveillance bugs installed throughout his apartment, Will introduces himself to his neighbor Andy and asks if he can stay with her. Andy confesses she’s fascinated by Will’s cloak-and-dagger life, and later observes Bloom snooping in Will's apartment.
Kale informs Will that Spangler knows they're working together.
News of Tanaz's murder reaches API just after Tanya is sent to rehab after failing a drug test. Julia Harwell is brought in to help with the analysis. The team learns Kateb survived the missile strike.
Will tracks down Katherine and tells her everything he’s learned about Atlas MacDowell, the crossword puzzles and the four-leaf clover. Katherine reveals a four-leaf clover was found near Tom and Gerald’s bodies.
In API's library, Will cross-references API white papers about world trouble spots with Atlas MacDowell business ventures. In the process, he learns David checked the same reports.
After Kateb disappears and Yuri and Boeck are murdered, Miles surmises a terrorist operation is in progress.
Despite Bloom’s warning to cease contact with Will, Katherine sends Will the beach photo with Tom, James, Spangler, and Bradley identified by name. Will explains his theory that Atlas MacDowell uses API intelligence to cause and capitalize on world crises for profit. If Tom, like Gerald Bradley, killed himself out of remorse, another catastrophe could be imminent.
Grant theorizes that Kateb is an extremist convert. Further analysis suggests he’s Joseph Purcell, a twentysomething male from New Jersey who studied in Yemen and recently reentered the United States.
Spangler instructs Roy to eliminate Will; Roy tells Bloom to make it look like a drug overdose. At Will’s apartment, Bloom and Will struggle until Will shoots Bloom in the head. Stunned and bloodied, Will calls Kale who has the body and the evidence removed.
After hearing about the failed attempt on Will’s life, Spangler's associates demand that their latest operation be aborted. Spangler contends it’s too late.
At API, Spangler announces that finding Purcell is a priority and assigns Will and Grant to work from a field office in New Jersey. Will crosschecks Tanaz's records and realizes that Bloom always met with her after visiting Houston. Kale then informs Will that "The Houston Problem" white paper analyzed the possible crippling effect on U.S. oil supplies should a tanker be sunk in Galveston Bay. Putting the two together, Will determines that Galveston Bay is Purcell’s likely target, but it’s too late: Purcell has already reached Texas and loaded missiles onto a small pleasure boat. News reports emerge describing the bombing of an American tanker in Galveston Bay.
Katherine tells Will about a movie Tom referred to in a cryptic note she discovered. Will insists she find the DVD. Katherine leaves the safe house where she’d been staying and discovers that the DVD has footage of Tom implicating Spangler along with a message for Will from David. Katherine calls Will and they agree to meet in Central Park.
Spangler's co-conspirator Joshua Lowan again demands the whole operation be shut down. Spangler resists, saying Iranians will be blamed for the attack.
At API, Will becomes suspicious because the evidence too conveniently implicates the Iranians, while Grant accepts the evidence at face value. Spangler promotes Grant to team leader.
Before going to the park, Katherine visits an address Tom mentioned in the DVD and finds Andy who accompanies her to Central Park. As Katherine waits for Will, Edward Roy kills her by sticking her with a syringe.
Back at API, Will pieces together evidence proving that Bloom flew to Houston on an Atlas MacDowell subsidiary's plane, thus linking Spangler to the conspiracy. Spangler, meanwhile, receives an envelope containing a four-leaf clover.
Will confronts Spangler on API's roof and reveals everything he’s uncovered about the conspiracy. Spangler challenges Will to report his findings. After Spangler departs, Will sees the API director's four-leaf clover on the roof's ledge.