An ambulance drives away from Binghamton, NY, and holds a single prisoner, Marcus Ayers. Marcus slips a quarter into his mouth and carefully observes and calculates every variable of the ambulance, the agents guarding him, and the surrounding cars. He then takes the coin and flips it toward an IV stand. He knocks it into a drawer, opening the door and dropping an oxygen tank onto his guard. The tank sprays gas into the driver’s face, he goes out of control, and slams into several cars. A loose pipe on a truck shoots through the windshield, shatters Marcus’ handcuffs, and breaks open the rear door of the ambulance. Marcus casually gets out, picks up his coin, and goes to call in the accident at a nearby pay phone.
The Alpha teams moves into their new offices. To nobody’s surprise, Nina has already convinced the decorators to finish her office. Rachel enhances her vision and realizes that her new office is (microscopically) filthy. Bill moves the pop machine but Gary still complains about a hum even though it isn’t plugged in yet and Rachel can’t hear anything. Disgusted, Bill leaves the pop machine in the middle of the room and goes. Meanwhile, Rachel gets a call from her mother and takes it despite promising herself that she wouldn’t. Gary listens in with his ability until Rachel hangs up.
Cameron arrives and gets the last office, and asks Nina what they do. She explains that they spend most of their time finding other Alphas. The government tracks them and sends some to the “Compound” in Binghamton, and Gary notes that they don’t have to worry about going there but Cameron does.
A woman, Bonita, arrives with extra office keys for Rosen. Rosen arrives and explains that Bonita is their real estate agent. As he leads her away, Bonita returns his tie that he left at her place the previous night. Rosen gets a call from Dr. Vijal Singh, the head of research at the Compound, summoning him to the crash site. The doctor realizes immediately that Marcus is the one who engineered the crash so he could escape, and admits that Marcus has refused to talk to him for years. Singh warns that Marcus’ mental condition has gotten worse. Nathan Cley, head of Binghamton security, comes over and Rosen insists that he knows how Marcus can think and that he can help. Cley refuses his help, figuring all they need to do is figure where Marcus is going. Rosen warns that Marcus analyzes moves and is always attacking, and his paranoia means that he sees enemies everywhere. He’s perceived a problem and has broken out to fix it, and they have to figure out who or what the problem is. As Singh and Cley go to the ambulance, Rosen examines the nearby pay phone and realizes that Marcus has sketched a symbol of a chess piece, a knight, on the glass.
Seven years earlier, Rosen and Marcus play chess in the park. Marcus explains that people always make perfect moves, even if it’s only perfect for them. Rosen warns him that he’s wrong to believe that everything happens from clear intend, and that sometimes things are as random as a flip of a coin. When the doctor notes that no one caused Marcus to become his patient, Marcus points out that his roommates don’t like him, they threw a party, Marcus got mad, and the judge sentenced him to treatment with Rosen. Marcus believes that his roommates planned the entire thing and wonders how Rosen can’t see that. The doctor explains that his brain scans revealed a unique neurological anatomy and asks if there is anything extraordinary he can do. Marcus takes Rosen’s hand and holds it up just as a leaf blows into it.
In the present, Rosen goes to the park and finds the leaf lying on the chessboard. As he approaches it, Marcus watches from hiding. Rosen lifts the leaf and finds the quarter beneath it.
As Nina and Rachel leave the office, Rachel is on the phone arguing with her mother again about the boy her parents set her up with. When her mother hangs up, Rachel figures that Nina would have handled it better. Nina notes that she hasn’t seen her family in years and Rachel shouldn’t use her as an example. Nina then drives over in a “borrowed” car and chats with Cameron. She tries to reassure him that he belongs there and Rosen believes in him.
The next day, another woman arrives and asks for Rosen. Bill assumes she’s another of Rosen’s romantic interests, but the woman reveals that she knows all about their abilities. Rosen arrives and explains that the woman, Kathy Sullivan, is their new DoD liaison while Don Wilson is on assignment. The doctor calls them into the conference room for their new case. However, Sullivan talks to him privately first and warns that Marcus blamed Rosen for his imprisonment at Binghamton. Rosen doesn’t believe that Marcus wants him dead and informs Sullivan that Marcus left him a message at the accident site. She warns him that he has a conflict of interest but Rosen disagrees. The liaison backs off and says that she doesn’t plan to play games with him, but Rosen informs her that he didn’t plan to use his Alphas for government work. However, he says that’s the situation and they have to deal with it.
Rosen briefs the team on Marcus, informing them that he can predict and control cause and effect in the physical world. As the others leave, Nina asks why Rosen didn’t tell her about Marcus’ escape, and that she knows that Rosen sending Marcus there bothered him. She reminds Rosen of what happened to her boyfriend and she has always worried that she and Bill would be the next ones sent to Binghamton. Rosen assures her that he worries about those decisions every day.
Cameron watches tapes of Marcus testing his abilities and warns Rosen that Marcus has a mean streak. Rosen admits that since Marcus can control much of his environment, he doesn’t understand when others can’t. The doctor notes that Cameron’s hyperkinesis is similar to Marcus’ ability. However, Marcus blames everyone else for what goes wrong in his life, while Cameron blames himself. Cameron disagrees, figuring that Marcus blames himself.
Rachel analyzes the coin and finds a trace of ash. Rosen isn’t surprised and tells her that it represents past failures. He then goes to an apartment building.
Six years earlier, Rosen goes to the same building. The fire department is there after a gas leak exploded. Rosen spots a coin lying in the ash and picks it up.
Now, Marcus approaches Rosen and asks what took him so long. He wonders where Rosen’s team is and the doctor assures him that the only enemy Marcus has is himself. Marcus says that Singh and his team spent six years telling him the same thing, and that Rosen is the one who handed him over to Singh. Rosen objects, saying that they just want to heal Marcus. However, Marcus tells them that things have changed and Binghamton has big plans for the future. He realizes that Rosen doesn’t know what is going on at Binghamton nor that he’s being used as bait. Cley and his people move in and Marcus throws his bottle of pop into the path of a skater. He goes out of control, diverting a truck into a scaffold holding concrete bricks. The bricks fall on two of the agents and Marcus escapes in the confusion.
Back at the office, Cley blames Rosen for keeping them out of the loop. Sullivan tries to get them to work together, but Rosen asks Cley what is going on at Binghamton. Nathan dismisses Marcus as a paranoid and leaves to call his dead agent’s next of kin. Rosen tells Sullivan that Marcus’ delusions may have a basis in truth and could lead them to Marcus himself. They go to see Singh at a restaurant and ask if Marcus’ treatment was modified. Singh finally admits they were sending Marcus off-site to surgically suppress his ability. Rosen warns that Marcus’ ability is an integral part of him, but Singh notes that if they had succeeded then the agent wouldn’t be dead. When Rosen objects, Singh ask if he sent Marcus to him to get rid of him and figures that Rosen prefers not knowing what goes on at Binghamton.
As Singh goes outside, he finds a black rook in the water-filled gutter. As he picks it up, two men unstring metal wire as a luggage cart rolls toward him.
Sullivan and Rosen hear the sound of a car crash and run outside. Singh has been yanked up on the wire and pierced. Rosen finds the black rook on the sidewalk.
As the Alpha team examines the street, Rosen shows Sullivan the chess piece. She vows that Marcus’ “game” will only end with his death. Meanwhile, Cameron uses his own ability to recreate how Marcus set up Singh’s death. He finds the quarter that Marcus used to set off the chain of events and shows it to Rosen and the others. Rachel doesn’t find anything on the coin, while Nina has no luck talking to the witnesses. Rosen shows them the chess piece and Bill figures that Marcus will go after the black king next. Meanwhile, Rachel examines the black rook and finds pollen on it. Back at the office, she determines that the pollen is from stargazer lilies. Bill has Gary do a search of cameras for stargazer lilies. Meanwhile, Rosen examines photos of Marcus and contemplates the black rook.
Six years ago, Rosen gives Marcus a cup of coffee and shows him the ash-covered coin and asks him what happened in the apartment. Marcus dismisses the gas-main explosion as an accident, but then says that his roommates were only injured, not killed. He’s confident that no one would have died unless he wanted them to. Rosen tells Marcus that he needs more help then he can provide. The Alpha starts to pass out as he realizes that Rosen drugged his coffee. Cley and his people arrive to take him to Binghamton.
Now, Bill warns Rosen that he can’t blame himself for Marcus’ actions and Marcus was born broken. Rosen doesn’t see it that way but Bill promises that they’ll stop him. Gary comes in and tells Bill that he needs to be specific. He confirms that he’s correlated the lilies to people involved in the case and located the flower sin the lobby of the building where Cley and his people are temporarily located.
Cley finds a black king chess piece next to the lilies in the lobby. Rosen warns him that Marcus is still there, but Cley is happy that Marcus will come after him so they can finally capture him. He goes out to the middle of the lawn and dares Marcus to do his worse.
Rosen, Sullivan, and the Alphas go to the building. Cameron points out that Cley has chosen a perfect spot with very little for Marcus to work with. Rachel spots the snipers on the roof, but Rosen warns that Marcus will have seen it all coming a mile away. Bill and Rachel fan out in on direction while Cameron and Nina go a different way. As she leaves, Nina objects to the plan to assassinate Marcus. She warns Rosen that she didn’t sign up for the murder of Alphas.
Bill and Rachel spot Marcus at the gas mains. He runs off and Rachel smells gas in the sewer. Cley’s agents fire at the fleeing Marcus and ignite the gas, setting off a series of explosions. Bill gets Rachel to safety, while Cameron gets Nina out of harm’s way just in time.
In the confusion, Marcus grabs Rosen at knifepoint and forces him to drive away in a government SUV. Rosen wonders why Marcus wants him now and the Alpha says that he has something to show him.
Rachel has Gary track the SUV and Bill drives after it. Meanwhile, Cley and his people secretly follow them.
Marcus has Rosen drive to a bridge overlooking the park where they played chess. He tells the doctor that they all have reason to be scared no matter what side they are on. When Rosen points out that he broke the law, Marcus explains that the people at Binghamton plan to do something that defies common decency, and that Singh is a victim of war. He realizes that Rosen has no idea what’s coming and that the Alphas are an out-of-context problem. No one saw them coming so the instinctive response is violence. Rosen insists that the Alpha phenomenon is a gift for all of them, but Marcus insists that Singh wanted to turn him and all of the Alphas into nothing. Rosen believes that things can be changed but Marcus says that he is locked in. He believes that Rosen is the variable and can make the one move that will get him to the future he wants. When Rosen asks what the move is, Marcus tells him to kick over the chessboard.
Bill and the others arrive and Marcus tells Rosen that things are playing out the way he planned. Cley pulls up and Marcus tells Rosen that if he’s wrong, they’ll take him alive. He then shoves Rosen away and drops the knife. Cley shoots him in the chest and Marcus falls backward into the river below.
Later, Rosen and Sullivan visit the park. There’s no sign of Marcus’ body, but Sullivan figures that Cley shot and killed the Alpha and his body was washed away. Rosen asks her about an out-of-context problem and Sullivan compares it to the Aztecs, who were destroyed by the invading Spaniards. Rosen warns that they can’t an us-vs.-them mindset. As they go, Cley continues his search of the river, unaware that there’s a quarter in the water below him… with Cley’s bullet imbedded in it.