Darwyn Al-Sayeed (Michael Ealy) is an FBI agent working deep undercover. He's been posing as a prisoner, and on his release, a radical Islamic mentor (Martin Dorsla) gives Darwyn an address that turns out to be a synagogue, where he finds Farik (Oded Fehr), who is posing as a Jew, but is actually the leader of a terrorist Sleeper Cell, who says he's "putting together a team of holy warriors--believers who are prepared to strike without warning, without pity." That night, Darwyn is met by cell member Bobby Habib (screenwriter/actor Grant Heslov of Good Night, and Good Luck) and they are assigned surveillance on a local Muslim girl who sneaks out of her house to go to a frat party. Bobby is an affable wisecracking sort of guy, and invites Darwyn to his little daughter's birthday party that weekend. There, he meets Bobby's attractive neighbor, Gayle (Melissa Sagemiller), a single mom. They seem to click, and Darwyn lets her know quickly that he's an ex-con trying to get his life together. She still seems interested. Later that day, Darwyn meets with the other members of the cell. Christian (Alex Nesic) is a French former skinhead. Tommy (Blake Shields) looks like the All-American boy, and is a Qu'ran scholar. Ilija (Henri Lubatti) is from Bosnia, and tells Darwyn how his family was murdered by the Serbs, and he was then found and raised by the Mujahideen. "I loved America, man" he tells Darwyn, "but you never came. Not for us." Later that night, Darwyn, against his better judgement, sees Gayle again. They see a news story that reveals the purpose of his "surveillance" mission. He's called away when Farik stages an emergency meeting out in the desert, and announces that there's a traitor in the group.

Darwyn Al-Sayeed (Michael Ealy) meets with Ray (James LeGros), his FBI handler, who wants to know where Bobby Habib and his family are. Darwyn deflects the question, complaining about the FBI losing the group when they drove out into the desert. Later, Darwyn asks Farik (Oded Fehr) what happened to Bobby's family. Farik is reluctant to tell Darwyn anything he doesn't need to know, but tells him the family was sent back to Egypt. He's sent to the mall on a recon mission with Tommy (Blake Shields), who keeps getting a call on his cell phone from someone named "Lynn" that he refuses to answer. He later tells Darwyn that it's his mother, a professor at Berkeley, and that he's worried she'll come snooping around. Darwyn has to do some quick thinking when Tommy notices that they're being followed. Farik goes to USC in an effort to recruit Eddy (Jeff Mallare), an Indonesian microbiology student. Eddy is not interested in joining the cell, claiming that his fight is in Jakarta, but under pressure from Farik, he does provide him with some necessary materials. Gayle (Melissa Sagemiller) asks Darwyn what happened to Bobby Habib, and he claims ignorance. She also tells him that the father of her son Marcus (Jake Soldera) died in a drunk driving accident. Darwyn gradually comes to understand that Farik is planning an anthrax attack on the West Side Galleria, and warns Ray, but the plan goes in motion must sooner than they had anticipated.

Ray (James LeGros) has to defend Darwyn (Michael Ealy) and explain the shooting of Bobby Habib to his bosses, who are considering ending the operation and making an arrest immediately. Darwyn apologizes to Gayle (Melissa Sagemiller) for standing her up, but he is forced to continue to lie to her. Farik (Oded Fehr) tells the cell that their funding in Mexico has hit a snag, and because Darwyn and Christian (Alex Nesic) speak Spanish, he takes them down there with him to straighten things out. Farik has to deal with a drug dealer/gun runner/pimp named Felix (Eduardo Yáñez) who wants a much bigger cut of the profits, and knows exactly what Farik is using the money for. Darwyn is appalled to learn that Felix is kidnapping underage children to sell to depraved tourists, and demands that Farik put a stop to it. On returning to the U.S., Darwyn is intercepted by Ray, who tells him that the operation was going to be shut down until the bureau discovered the existence of two more potential cells in Washington and New York.

Darwyn (Michael Ealy) once again reconciles with Gayle (Melissa Sagemiller). This time Farik (Oded Fehr) is watching him, and warns him, "romantic relationships complicate our mission." Farik strong-arms Eddy (Jeff Mallare), convincing him to fly to Vancouver in order to test a batch of anthrax and then smuggle it back into the U.S. Darwyn sneaks his cell phone into Eddy's luggage, so the FBI will able to track him with the GPS device, and calls Ray (James LeGros) to let him know what's going on. Ilija (Henri Lubatti) accompanies Eddy on the flight, but once they have the anthrax, Eddy will drive it back over the border in an RV. While at the airport, Farik and Darwyn go to arrivals, where they see influential Islamic scholar Zayd Abdal Malik (Marc Casabani) coming in from Yemen. Farik orders the members of the sleeper cell to attend a speech Malik is giving at a local mosque. Malik talks about the evils of terrorism, decrying those who use the label Islam to murder. Tommy (Blake Shields) walks out in disgust, but Christian (Alex Nesic) seems genuinely intrigued by the man's words. Darwyn is worried the Farik plans to murder Malik, who has worked to "deprogram" terrorists in the Middle East, but Ray suspects that Malik is a fraud who is secretly working with Islamic extremists. Meanwhile, agents in Canada have to come up with a way to make sure that the anthrax doesn't get across the border, without blowing Darwyn's cover.

After losing the anthrax shipment, Farik (Oded Fehr) gets a warning from his handlers. He'll be killed if he fails again. He's given a new assignment, and assigns each member of the cell a specific task. Darwyn (Michael Ealy) has to get custom-made tires which would be impervious to bullets. Christian (Alex Nesic) has to procure a bunch of dogs. Tommy (Blake Shields) trains to drive a big rig truck, while Farik and Ilija (Henri Lubatti) case a warehouse with a very heavy security system. It turns out that Kenneth Bin Al-Waleed (John Siciliano) is using the space to train fighters for the insurgency in Iraq. But Farik needs the space for his own purposes. He assigns his team to pose as would-be insurgents and train with Kenneth so they can recon the warehouse and get the security codes. Ray (James LeGros) gives Darwyn a lecture about his relationship with Gayle (Melissa Sagemiller), warning him that he's putting her and her son at risk. But Darwyn still joins Gayle and Marcus (Jake Soldera) for dinner at the home of Gayle's sister, Catherine (Eden Rountree), where he gets into an argument with Catherine's bigoted ex-husband. On entering the warehouse for "training," the four cell members are told that they can't have any contact with the outside world for the next month. After a couple of days (during which both Ray and Gayle grow increasingly distressed about Darwyn's lack of communication), Ilija figures out the security codes and contacts Farik. But Kenneth is not prepared to let his base be used as a headquarters for a terrorist group.

Farik (Oded Fehr) convinces the owner of a chemical plant to use Xpert Security (Farik's cover job) to do background checks on all of his employees. He uses that information to target an unhappy worker, Ernest Jefferson, who might be amenable to procuring some phosgene, which turns into a toxic gas at room temperature. Darwyn (Michael Ealy) befriends Jefferson, and eventually convinces him to sell him the phosgene, which he claims he needs for a home remodeling job. Darwyn also pays a visit to his mother. He also visits Marcus's (Jake Soldera) school, to be the boy's special guest for show and tell. But later he gets some surprising information about Gayle (Melissa Sagemiller) from Ray (James LeGros). It turns out that Gayle's husband is not dead, but in San Quentin on a drug charge. Again, Ray tries to convince Darwyn to end the relationship. Tommy (Blake Shields) gets an unwelcome surprise visit from his mother, Lynn (Ally Walker), who is in town for a symposium. He snubs her, sending her into the surprisingly sympathetic arms of Christian (Alex Nesic). Farik performs a little experiment at Dodger Stadium, and later, tests out his chemical weapon on the dogs that his crew procured. "The dogs we'll target next," he tells them, "have two legs instead of four."

Farik (Oded Fehr) travels to Las Vegas and meets with the leaders of the New York and Washington sleeper cells to strategize, and leaves the crew with explicit instructions for their next move. Darwyn (Michael Ealy) finally breaks it off with Gayle (Melissa Sagemiller), telling her that it's because she lied about her husband. An Afghan teen, Khashul (Luis Chávez) shows up at the warehouse to train with Ken, who is dead, of course. Uncertain as to what to do with the boy, the crew allows Darwyn to look after him until Farik returns. Darwyn eventually learns that Khashul was taken from his home and wrongfully imprisoned in Guantanamo Bay for three years, where, he says, "Mostly I learn to hate Americans." Darwyn tries to show the boy a different view of Islam, and his lessons seem to be sinking in. Darwyn contacts an ex-girlfriend at the State Department, trying to arrange for Khashul to go back to his homeland. But the others find out that Khashul has been at Gitmo, and Farik, concerned that the boy might be on a Homeland Security watch list, orders him killed. Still reeling from the breakup, Gayle gets a visit from Bobby Habib's cousin, Abbas (Amro Salama), who questions her about Bobby's whereabouts. Concerned that he might have been taken away by the authorities, he asks Gayle if Bobby had any contact with extremists or potential terrorists, and that gets Gayle to thinking.

Darwyn (Michael Ealy) watches Ray's funeral from a distance. Thanks to Gayle (Melissa Sagemiller), Darwyn's now being watched by an overzealous LAPD detective, Moss (Michael Cudlitz of Band of Brothers). The LAPD talk to one of Darwyn's fellow inmates, who eventually manages to get word back to Farik (Oded Fehr) that the police are interested. SA Patrice Serxner (Sonya Walger) takes over as Darwyn's handler, and immediately rubs him the wrong way by criticizing Ray's work. She also upbraids him for going to Ray's funeral, but Darwyn. Ignoring her, Darwyn pays a consoling visit to Ray's widow. Moss gets a warrant and has Darwyn's apartment searched while he's out, and the cops are sloppy enough that Darwyn knows someone was there. He confronts Serxner about it, and she eventually discovers that the LAPD is watching Darwyn. She tells them to terminate their investigation. They think it's about turf, so they don't listen. Farik finds out that it was Gayle who put the cops on Darwyn, and uses a cattle prod on Darwyn to find out what he told her. Darwyn convinces Farik that he didn't tell her anything, but Farik still pays a visit to Gayle. Later, as Farik and the crew are meeting with a gang of white supremacists, dealing Afghan heroin in exchange for explosives, the LAPD decides to move in.

Darwyn (Michael Ealy) and Farik (Oded Fehr) track Jim (Brad Greenquist), a trucker who is carrying a shipment of phosgene from Los Angeles to Newark. They intercept him when he stops at a motel to do business with a hooker. Pretending to be cops, they take Jim prisoner. Farik wires an explosive device to the truck, "just in case," so Darwyn has to surreptitiously phone his handlers to make sure they know to let the truck through. They bring Jim back to the warehouse, where Farik threatens to hurt his wife and child if Jim doesn't make daily calls to his dispatcher to tell them he is en route. Patrice (Sonya Walger) learns more about Farik's background from a captured terrorist. Farik gets an urgent call from his wife, Samia (Susan Pari), who has surprised him by coming to L.A. Darwyn convinces Farik to let the cell members have one last night on the town while he's away. Tommy (Blake Shields) agrees to stay behind to guard Jim. Christian (Alex Nesic) goes to a strip club before phoning his wife to leave a tearful goodbye message. Ilija (Henri Lubatti) goes to a karaoke bar for one last tribute to A Tribe Called Quest. Darwyn meets up with Patrice, and tells her the phosgene attack will take place on a Muslim holy day in two days, but he's still not sure of the location. Meanwhile, Farik begs his wife to let him do his "duty." "You're the only person who has a hope in hell of making me change my mind," he tells her, "and I can't." Later, Farik reveals the target, Dodger Stadium, and explains that simultaneous attacks will take place in two other cities. Darwyn also finds out he got the calendar wrong. The attack will take place tomorrow.

On the finale of Showtime's miniseries, Sleeper Cell, "Judgment Day" has arrived. White House insiders, having gotten the wrong timetable from Darwyn (Michael Ealy), are debating about whether or not to alert local governments about the planned attack in Los Angeles. They decide to wait until they have more information about what the cells in New York and Washington are plotting. A chemical weapons expert tells them that if the attack goes off in a crowded area, there could be more than 10,000 casualties. The members of the cell videotape their final messages, with Darwyn pointedly noting, "Everything I've done, and everything I'm about to do I do for Islam." Farik (Oded Fehr), having destroyed all of the team's communication devices, causes a diversion by blowing up the front gate of the warehouse. The cell races out in their dummy emergency vehicle. Patrice (Sonya Walger) realizes what's going on, but it's too late and the cell has gotten away. But Darwyn manages to leave a message behind for the authorities to find, to let them know the location of the terrorist attack. At the stadium, Ilija (Henri Lubatti) has been assigned to start the fire that will bring the emergency call. Tommy (Blake Shields), Christian (Alex Nesic), and Darwyn are supposed to block the roads leading to the stadium by shooting at random motorists, while Farik has the "honor" of driving the emergency vehicle loaded with phosgene into the stadium.