In the middle of the night, KITT scans radio frequencies. After triangulating a location, KITT wakes Mike at 4:17 A.M. to alert him to a possible situation. When Sarah gets to the SSC, Billy and Zoe are already on the case. A plane has disappeared, and Mike and KITT are nearing its last known GPS location. When Mike suggests that Sarah take KITT to task for waking him up at 4 A.M., KITT autobrakes, sending Mike's head thumping into the dashboard.
When KITT stops at a smoking crater containing the remains of a Lear jet, Mike orders him to call the NTSB. KITT protests: the jet's crash radius is too small, there are traces of explosives in the wreck, and the tree line is still intact. KITT thinks a second party faked the crash. When Mike asks why someone would go to such trouble, KITT reminds that's what they get paid to figure out. Mike struggles with a revelation -- KITT gets paid?!
Mike has KITT run the plane's call numbers as DEA Agent Jessie Renning shows up with her team, whom she orders to secure the crash site. Mike claims he was out four-wheeling when he stumbled across the crash, just as KITT informs that the jet is registered to the DEA. Mike tells Renning that the crash was faked -- what was on that plane? Renning dismisses him and walks off.
Billy tracks the plane to discover that it had five passengers: two DEA pilots, two DEA agents, and ten-year-old boy genius Danny Clark. Mathlete Danny has information on Peruvian drug king Esteban Bahia, who's extremely dangerous. Mike tells Sarah that he'll find the plane, then orders KITT to locate possible destinations and find all relevant information on the pilots and agents on board.
When the DEA database dead ends, Zoe and Billy tap into the police department. The DEA took Danny into custody when he called in the murder of his father Jake by Bahia. Billy assumes Danny must already be dead. Zoe informs that his parents are separated, and leaves to question his mother, Amy. Finding a possible location for the jet, KITT sets a course for the Jamison Canyon Airstrip.
Amy answers the door with gun drawn. Zoe explains that the DEA faked the crash and that Bahia has Danny. Amy finally ushers Zoe inside to explain that Jake, who worked for Bahia, had a big plan in the works, which he promised would take care of her and Danny forever. Danny wouldn't tell if he knew anything until being safely reunited with Amy. Concluding that Danny must still be alive, Zoe calls Mike.
Mike concludes that Bahia is trying to get info out of Danny as they speak, and tells Zoe to protect Amy. Why did the DEA leave her alone? KITT locates the jet in a hangar on the airfield. The cell phone signals of the DEA agents who were in the jet lead him to a shipping container. Mike orders KITT to laser off the container's lock, only to find the two agents bound, gagged and dead.
The DEA pilots are nowhere to be found. Ordering KITT to use facial recognition to search all traffic cameras for Danny, Mike calls Renning, who demands to know how he got her number. He's guessing the pilot betrayed the agents and signed on with Bahia. Renning asks if one of the agents was named Wesley. When Mike confirms, she hangs up on him, and has his phone number tracked.
In the meantime, KITT locates a silent video from a gas station security camera. Danny escapes Bahia, runs to a security camera and shouts a message. Bahia shoots the attendant, grabs Danny and drives off. KITT calls police, sets to tracking Bahia's SUV, and starts recreating Danny's message to the camera. KITT calculates 43 minutes to interception of Bahia.
Zoe and Amy watch an old home video featuring Danny, a veritable engineering genius. Zoe promises a dubious Amy that Mike is the best; he'll get Danny back. With Bahia's SUV in sight, KITT warns that intercepting Danny will be difficult; surprise is the only thing on their side. Mike orders KITT to deploy an EMT blast, which effectively stops Bahia's SUV.
KITT determines that the DEA pilots are in the car along with two armed henchman. Mike pretends to offer the pilots help with the engine, then knocks one of them out and shoots a henchman. With his gun to the second pilot's head, Mike introduces himself to Danny, promising he's here to help. Danny claims that all he wants to do is go to his room in his dad's house.
Bahia doesn't care if Mike shoots the pilot and refuses his offer to drive away in KITT. Ordering his remaining goon Valdivia to flag down a mini-van, Bahia shoots out KITT's tires and escapes with Danny, promising to kill him if Mike follows. Mike knocks out the second pilot and climbs back in KITT, who has translated Danny's security camera message: "He just wants his shipment back. He'll kill me after he has it. Read the writing on the wall."
Mike calls Sarah, who deduces that Danny's father Jake stole Bahia's latest shipment, hid it, and told Danny where it was before he was killed. Mike is convinced that the location of the shipment is written on the wall of Danny's bedroom in Jake's house, and Billy takes off to find it. Renning drives up and arrests Mike for interfering with a government investigation. KITT offers to help, but Mike tells him to stand down.
KITT calls Sarah with news that Mike has been arrested, and he's being towed to the impound lot. Disgusted, Sarah orders KITT to free himself, free Mike and find Danny. When KITT points out that he and Mike will be fugitives, Sarah promises to take care of it. Following Mike's earwig signal, KITT hacks into Renning's ROAMSTAR system and takes control of her car, enabling Mike to simply walk away. Dazed, Renning calls in an APB on KITT and Mike.
Mike asks KITT to use his 3-D generator to make a handcuff key, while disguising himself as a 1969 Mustang -- incognito! Sarah calls her dad's old friend, Darrel Armstrong, Deputy Director of National Intelligence to ask for autonomy to work in cooperation with the DEA's agenda. If it wasn't for Mike, Renning would still be investigating the plane crash. Armstrong spells it out: if Danny dies, Mike will be charged.
Sarah relays her phone call with Armstrong to Mike: it was the only way she could get him some wiggle room. Meanwhile, Danny has taken Bahia to a location in the woods where Valdivia starts digging. Back at Amy's, Zoe hears a dog barking. She takes out her gun and sends Amy out the back door -- into the arms of Bahia's henchmen.
When Bahia suspects that Danny is lying, he puts the phone to his head. Tied up in a van, Amy tells Danny not to tell Bahia anything, then is knocked unconscious. Desperate, Danny promises to give Bahia the location of the shipment if he'll let Amy drive away safely. Billy finds an equation written on the wall of Billy's room, enabling KITT to deduce the location of Bahia's shipment, 19 miles away. Mike orders KITT into Attack Mode; they have to get there before Bahia.
Hidden, Mike watches as Valdivia digs to find a box filled with cocaine. Mike orders KITT to explode the bomb he's planted in the box, shoots some henchmen, and yells for Danny and Amy to climb into KITT. Danny tells KITT they can't leave Mike, but KITT has his orders. Danny tells KITT to forget his orders and think for himself. KITT heads back to the scene, parks in front of Bahia's mini-van and opens fire.
Mike punches a dazed Bahia, takes his gun, and pulls him out of the mini-van. Danny runs up to pick up the gun and aim at Bahia. Mike talks Danny down, invoking the story of his own mother's murder, when he had to stand down. Taking a life won't bring Jake back. When Renning shows up to take Danny and Amy into custody, Danny pleads for Mike. Renning doesn't arrest Mike, but if she ever sees him again, she will.
Back at the SSC, Sarah reminds the team that they're no longer an official government operation -- Mike's on his own in the field, and should try not to piss people off. After an elated Danny tours the SSC, Mike hands over a bag of cash, the DEA's reward for the apprehension of Bahia. Amy tries to refuse, but Mike insists the money will help them start a new life. Sarah offers Danny a greater gift -- KITT will give him a ride home.