A plane explodes and crashlands into the Atlantic, killing all 345 passengers and crew onboard; amongst the fatalities are Mac’s wife, daughter-in-law and two of his grandchildren. In the aftermath of the crash, troubled adolescent Fahim bin Hassam overhears his parents Hassam and Yasmin arguing about Hassam’s dealings with the airliner that owned the doomed plane. The next day, Fahim discovers that Yasmin has disappeared. Fahim calls a hotline and begins to explain what he knows of his father’s involvement, but loses his nerve and hangs up before he can say anything incriminating. Mac, who is investigating the crash, hears Fahim’s call and performs a background check, learning of Yasmin’s disappearance and Fahim’s uncle Asif’s status on the TSA’s no-fly list. Feeling that the information adds up to a case worth looking into, Mac accompanies Lauren and Jake on a mission to befriend Fahim to obtain information from him.
After earning Fahim’s trust by protecting him from a gang of bullies, Lauren and Jake ask Fahim to help them collect evidence against Hassam. After Jake inadvertently mentions CHERUB’s name, Fahim agrees to help in return for an opportunity to sit the entrance exam if his father is prosecuted. Lauren and Jake infiltrate the bin Hassam household and plant listening devices in Hassam’s office. A week of surveillance uncovers nothing incriminating and Mac, suspecting that Fahim’s psychological problems caused him to panic after his mother’s disappearance, decides to wind the mission down. However, after Hassam discovers a relay for the listening devices he brutally interrogates the family’s cleaning lady, Sylvia.
Asif arrives Hassam declares that the security services on to their activities and prepares to kill Sylvia, but Fahim reveals that he allowed the house to be bugged. Asif tars the dick of Fahim and Hassam away to a warehouse and stays to retrieve passports and money while Fahim and Hassam flee to a safe house. On the way, Hassam admits that he killed Yasmin.
After being alerted by Fahim, Lauren and Rat (who had been visiting her) call an ambulance for Sylvia before heading to the warehouse and subjugating Asif. Meanwhile, Jake and Mac track down the safe house. Fahim tries to escape but is caught by Hassam, who holds him at knifepoint in a Mexican standoff with armed police. Jake sneaks up behind Hassam and surprises him, releasing Fahim. Hassam, unwilling to go to prison, claims to have a gun and is promptly shot dead by the police.
After Fahim is taken to hospital, Jake and Mac meet up with Lauren and Rat at the warehouse. When Lauren shows him a bag full of aeroplane parts, Mac realises that the bin Hassams were not terrorists as he had suspected, but had actually been buying expired plane parts and selling them on to airliners. A subsequent investigation into the plane crash reveals that damaged fuel valves caused a leak that led to an explosion, tearing a wing off the plane.
Back at campus, Fahim sits the entrance tests. Lauren goes to see Zara to provide a character reference, but Zara reveals that Fahim sleepwalks and talks in his sleep, making him unsuitable for recruitment to CHERUB; nonetheless, Mac decides to adopt Fahim. As they leave to break the news to Fahim, Mac gives Lauren a note written by his grandson moments before the crash, bidding farewell to his family.
In a subplot, James is dismayed to be given work experience at a local fried chicken restaurant, Deluxe Chicken, with Kerry. James and Kerry soon befriend co-worker Gemma Walker, who invites them and Dana to go clubbing with her and her boyfriend Danny Bach. However, at closing time James witnesses Danny threatening Gemma; when James intervenes, Danny tries attacking him and James knocks him out. A few days later, Gemma arrives at Deluxe Chicken with several bruises and Danny shows up to goad James into fighting him. Outraged, Kerry brutally beats Danny with a baseball bat, breaking his wrist and fracturing his shins. Zara uses her connections with a local inspector to help James and Kerry avoid prosecution, but gives the two decorating duty as punishment. While serving their punishment together Kerry admits that she still has feelings for James and the two kiss. However, James is unwilling to hurt Dana and stops Kerry. The two decide to remain friends.
· The scandal surrounding the faulty parts leads to the bankruptcy of the airline that owned the doomed plane, the removal of expired parts from 265 planes and a global investigation that results in the arrests of over 50 people.
· Asif is found guilty of the attempted murder of cleaning lady Sylvia Updike, who spends nine weeks in intensive care and nearly dies in hospital. He is sentenced to 15 years in prison. Asif and his wife Muna manage to avoid prosecution for shipment of the faulty parts due to complex evidence and different laws across countries, although prosecutors hope that they will eventually be brought to justice
· Fahim bin Hassam’s strict Abu Dhabi-based grandfather makes moves to both adopt Fahim and take control of Hassam bin Hassam’s assets; both requests are denied by authorities, who place Fahim in Mac’s care during Asif’s trial and freeze Hassam’s assets to pay compensation to crash victims.
· Mac returns to work at CHERUB on a voluntary basis assisting mission-control staff.
· Lauren’s mission performance is complimented; Jake, for his part, only misses out on his navy shirt for the mistakes he made in confronting the bullies and revealing CHERUB’s existence. Mac recommends that Jake sit refresher training before going out on another mission.
· Danny recovers from his injuries, only to find that two of his friends have taken over his gig bouncing at a local nightclub. When they refuse to give him a share of the profits he stabs both and goes on the run for three weeks before being arrested. He is initially charged with attempted murder but pleads guilty to a lesser offence and receives a seven-year sentence.
· Gemma is promoted to assistant manager at Deluxe Chicken. After breaking up with Danny shortly before his incarceration she spends several months in bed and breakfast accommodation before moving into a house with her younger sister Mel. She eventually loses contact with James and Kerry but they learn that she is expecting a third child with another boyfriend.
· James’ sixteenth birthday celebrations result in him, Dana and several other friends receiving decoration duty for vandalism and setting off fireworks.