He was working an undercover assignment of infiltrating a radical's militia group in the town bank of Sturgis, South Dakota, but ended in failure. Art was then removed from undercover duty and placed on 'rookie' assignments in surveillance by his boss, Joe Lomax.
He was called by his friend and partner Tommy Jordan who helped him to keep his job from Lomax. Tommy asked Art, about a missing a nine-year old boy who disappeared his parents were killed by an assassin. However, Art figured out the kid was still in the house.
Most of Chicago P.D. called it Murder-Suicide since they think the boys father killed his mother and himself. But Art doesn't by it, because the gun he is carrying cost over a thousand dollars. The suspect was a blue-collar worker, so he wouldn't be able to afford a gun like that in his salary.
Art soon found the kid, Simon Lynch was initially frightened and shocked up discovery. They brought him to a hospital, and the nurse told Art about Simon's condition and doubted he could answer any questions. Art figured the guy who killed Simon's parents is back so he took Simon out of the hospital to protect him. The reason why they're after Simon was because he cracked a top secret super code in a geek's puzzle magazine, NSA Agent Nicholas Kudrow sent in assassins to kill him, but luckily Art intercepted him and protected the kid himself.
His friend Tommy helped him out, but he had to keep low profile since the FBI thought he went rogue. Simon and Art went back to the house in the morning and reenacted how Simon parents were killed. It was the geeks puzzle magazine, that Simon figure out the government code and called the number. Art took it from here and made arrangements Dean Crandell to meet him in the Wrigley Building. He had to email him where to find him to talk. Art and Simon found the email in the library and meet him in the Wrigley building.
They both made friends with Stacey Siebring and Art ask her to watch Simon for a minute. Crandell explained why Simon's life in danger and his boss is a corrupt NSA agent who wants Simon dead for cracking the top secret code. Before Crandall was going to tell Art who is boss is, but he was killed in plain sight by the same assassin that was hired by Crandall's boss. Leo who worked with Dean and his best friend typed in a letter that their boss Nicholas Kudrow a corrupt NSA agent killed Simon's parents. He typed in carbon paper that is untraceable and has his finger prints on it.
He was going to deliver it to Jeffries, but it was too late. Art who made friends with Stacey and told him he was an FBI agent and Simon life is in danger. Leo's girlfriend saw his body and decide to send the letter Jeffries herself, he called Art's friend Tommy. She met Art and gave him the letter who is the mastermind behind this and this letter will have enough proof to put Kudrow behind bars. Art decide to see Kudrow for a minute and ask Tommy to put Simon witness protection. Art gives him 24 hours to call off the manhunt on Simon and tell the papers that his government was cracked by a nine year old autistic boy or he sends the letter to senate oversight committee that can put Kudrow behind bars. Art knows Kudrow is bluffing and he will give in Jeffries demands. Kudrow visited the FBI building played Art and Tommy's boss, Kudrow turn the tables on Jeffries by using his authority and the fact that Jordan arranged the Witness Protection under false pretenses.
He plans to have the NSA take over the protection for the meeting location. After Kudrow leaves, Jordan shows the evidence to Lomax and despite his initial doubts, Jordan confirms that the fingerprint markings on it were Pedranski's, now fully validating the evidence against Kudrow. Jeffries, with Jordan and a small FBI task force's help, sets a trap at the meeting spot. During the battle, Jordan protects Stacey, and the FBI team takes on Burrell, who is killed, trying to escape, when the windows blow out slashing his face open. Jeffries and Kudrow fight on the roof during which Simon walks to the edge of the roof and grabs Kudrow's gun, giving it to Jeffries and allowing him to take control as Jordan and the team come in.
In a last-ditch effort to get his victim back, Kudrow grabs Simon, is shot at point blank range by Jeffries, and subsequently falls to his death over the edge of the building. The case is over, Art is cleared on any wrongdoing and keeps his job as an undercover agent. Stacey drove Art to meet Simon at his new school and Simon is happy with his new foster parents that took him in. Simon owes Art his life and embrace him as his FBI agent friend.