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Scan is the 25th episode in the series and the 3rd in season 2. Michael and Lincoln experience car trouble as Mahone's pursuit of them goes up in flames; Sucre hits the road to stop Maricruz from taking a gamble; C-Note is determined to reunite with his wife and daughter despite their surveillance; a familiar face keeps a close eye on Sara, who finds the tables turned on her; determined to cash in on the prison break, Bellick partners with an unlikely ally.
The episode begins with Agent Mahone and other FBI agents investigating an exploded, upturned car. The agent standing beside Mahone comments on how sad it was that one of the fugitives had died so quickly since they had just broken out of prison and asks Mahone, "So which one of them was it?"
As Mahone stares at the remnants of the explosion, the agent next to him asks, "So which one of them was it?" Mahone replies, "Shales... Scofield, maybe Scofield." After Mahone walks off, Wheeler tells the agent that Oscar Shales was a fugitive that Mahone had never recaptured. Mahone grows more distressed and swallows some pills from his pen.
Twelve hours earlier, at the FBI field office in Chicago, Agent Mahone is told by one of his agents, Agent Lang, that all the hospitals and the fugitives' families are under surveillance but so far, none of the fugitives have been seen. After asking for Agent Lang's surname, Mahone informs her that a man on the run will make a mistake in the first 72 hours post-escape.
An agent brings in a backpack that the police got from a vagrant. In the backpack were items that included cell phones and the fake passports of Michael and Lincoln. Agent Mahone promptly tells the agents that Michael had made his first mistake. He then interrogates the man who stole the backpack from Michael's car, asking him what the car looked like. The vagrant tells him that it was grey, parked "15th somewhere", and was towed soon after he stole the bag.
Michael and Lincoln show up at Nika Volek's apartment unannounced. Michael barks orders to her to get some rubbing alcohol, towels, cayenne pepper and an alcoholic beverage (for drinking) to dull Lincoln's pain. Nika is distressed at Michael and Lincoln's presence at her home since the police had been there. After apologizing to Nika and asking her for some clean clothes for Lincoln, Michael leaves to retrieve their car. When Lincoln tells him to forget about the car, Michael tells him that he doesn't need a car, but that car because that car contains everything they need to disappear. However, when Michael returns to the place where he parked his car, all he could find was shattered glass.
Michael finds the place where his car was towed to and when he is asked to fill in the paperwork, the phone of the towing company rings. It is Mahone. Mahone asks Chuck, who was the employee attending to Michael, if he had seen a man asking for a grey Honda Accord with a busted side window. Chuck nervously and cryptically replies, "Yes, sir..." as Michael watches him. When Chuck turns around while speaking to Mahone, Michael grabs the keys from the counter, and is able to reacquire the vehicle before Mahone's police units can arrive.
While Sara is being released from the hospital, she recognises the nurse who is cutting off her nametag. The nurse tells Sara that she was the attending physician when she first started there. As Sara signs her release forms, the police come and inform her of her arrest. She is handcuffed and led out by two police officers, passing by Agent Kellerman who is watching them as he tells "Caroline" that he'll keep an eye on Sara. Governor Frank Tancredi pays his daughter's bail and meets his daughter at an interrogation room. He orders her to go to daily Narcotics Anonymous meetings and to place the blame of the escape incident on Warden Henry Pope. Before his departure, Governor Tancredi informs Sara that he will be sworn in as the Vice President of the United States in a week's time and that while she will be invited to his inauguration, she will not attend.
Bellick goes to a convenience store and while trying to buy beer and teriyaki jerky, sees his nemesis Geary working his new security guard job. They fight in the store, drink beer together, and Bellick becomes a bounty hunter and teams up with Geary after interrogating Manche Sanchez.
After hotwiring a vintage Chevrolet El Camino pickup in Defiance, Ohio and escaping a Pennsylvania State Trooper in Latrobe, Pennsylvania by climbing aboard a passing cargo train, Sucre arrives in Bedford-Stuyvesant, Brooklyn, New York, and discovers that Maricruz is getting married in Las Vegas and takes his friend, Petey's, motorcycle, a 1952 Ural.
C-Note makes a phone call to his scared and reluctant wife, telling her he'll be waiting in the "Rainbow Room" in the spot where they "took that beautiful picture." Mahone's team has a wiretap on the phone call and Agent Lang assumes that C-Note is referring to the Rainbow Room restaurant in Manhattan, New York and has C-Note's mugshots sent there. Later on, C-Note visits his daughter at recess and tells her to relay a message to her mom to turn on the porch light at 7pm if she plans to meet him. When he comes by the house, he hides across the street for a few minutes before his wife decides to turn on the porch light. The "Rainbow Room" is actually their daughter's bedroom, and the picture is a photograph hung on the wall next to the window. After turning on the porch light, his wife sits down to an interview with Agent Lang.
Michael and Lincoln take off from Nika's home in their car and make a turn when they reach Illinois Route 38. This is indicated in the tattoo on Michael's wrist which reads "38 12 1037" in the form of a barcode, where "38" referred to Route 38. After turning into Route 38, Michael resets the mileage counter. When the counter reaches 12, Michael stops in the middle of a bridge. "12" referred to the number of miles that it took to reach the bridge. Meanwhile, Agents Mahone and Wheeler track Michael and Lincoln's whereabouts through their cell phone. They noticed that they suddenly stopped, and speculate that they may be meeting someone there.
Unscrewing one part of the railings on the bridge, Michael and Lincoln stage a car accident after turning on the car radio and set it to "scan" so that when it reaches the frequency "103.7" (the last four numbers of the tattoo), it will trigger the bomb to explode. At the nick of time, just before Mahone and Wheeler arrive, the car explodes along with false corpses placed in the front seats of Michael's Honda Accord.
Nika arrives with her car and gives Michael her car keys. Michael thanks Nika and promises to pay her $10,000 once he and his brother reach Mexico plus $3,000 for the car. When Nika asks Michael if he is going to meet up with Sara, he says he doesn't know and hands the car keys to Lincoln, who proceeds to take care of the driving. They are spotted by Bellick and Geary as they're leaving.
- Scan refers to the scanning of the radio stations and a barcode scan which is what the tattoo on his right wrist is of.
- Oscar Shales, the name of the fugitive who Mahone never caught, is an anagram for "a search loss".
- The song the radio was playing before the car exploded was "Hush" by Deep Purple.
- The homeless man that Mahone intergates also appears in the 18th episode of Season 2, Wash.