Adolescents Andy and Stuart Pierce witness their mother Christine being attacked and blinded by animal rights activists. One leaves a stark warning for Christine, to quit her job at a nearby animal lab or be killed.
Lauren and Bethany devise a plan to sneak into the basic training compound to give care packages to Rat, Jake and the rest of the trainees. Lauren blackmails James into helping the two by threatening to tell Kerry that James cheated on her with Becky Little the year before. The three successfully sneak into the compound but are spotted by Mac on the back-up CCTV system. Mac, having realised that James was blackmailed, did not give him a punishment.
Two weeks later, Lauren goes to apologise to James. James forgives her, and reveals that Zara has asked him and Kyle to join her on a mission. James adds that they need a girl to complete the team, and invites her to the mission briefing. The mission requires Zara and the cherubs to pose as the wife and children of animal activist Ryan Quinn to infiltrate the Animal Freedom Militia (AFM), an ultra-extremist animal rights organisation that has attacked several employees and associates of animal research lab Malarek UK, including Christine Pierce.
Zara, Ryan and the cherubs relocate to Corbyn Copse, the village where Malarek's lab is located. Kyle befriends activists Tom and Viv Carter, whom Kyle discovers both sympathise with the AFM. Kyle also begins dating Tom. Meanwhile, Lauren develops a rapport with Ryan after realising she sympathises with his attitude towards animal exploitation. After Ryan and activists from his animal rights group, the Zebra Alliance, rescue a group of Beagle puppies from a local breeder, Lauren helps clean the dogs. Lauren decides to adopt one, whom she names Meatball.
After quitting the Zebra Alliance, Viv makes contact with several AFM members; their leader, Jo (who’s true identity is later revealed as Rhiannon Jules), also recruits James, Kyle and Tom. Jo announces that the AFM has been dissolved and reformed as the Animal Freedom Army (AFA), and orders James, Kyle and Tom to carry out an arson attack on the depot of a company that delivers animals to Malarek. Other members of the AFA attack the Malarek chairman with a car bomb. However, Jo realises that the attacks have not attracted enough attention and sends James along with AFA members Adelaide Kent and Kennet “Mark” Marcussen to abduct celebrity chef Nick Cobb, who commissioned Malarek to force-feed Cobb’s branded sink cleaner to rabbits as evidence in a lawsuit against Cobb. James hands Cobb over to Kyle and Jo before retreating to a safe house. Meanwhile, the AFA broadcast live footage of Viv and the other extremists force-feeding Cobb his own sink cleaner.
James overpowers Adelaide and Mark before giving the AFA’s location to Zara and driving away. The security services cut the AFA’s satellite link, alerting Jo. Kyle, realising that Cobb will soon die from shock, steals a rifle off a guard and forces the AFA to help Cobb into a van before driving to hospital. Zara and Lauren part ways with Ryan, who lets Lauren keep Meatball. Before leaving, Lauren tells Ryan that she has taken his words to heart and has become vegetarian.
As cherubs are not allowed to keep pets, Lauren gives Meatball to the Askers. Zara, who had applied to succeed Mac as CHERUB chairman, is given the job and is congratulated by the cherubs. James, Lauren and Kyle join Kerry, Bruce, Rat, Bethany and Jake at the summer hostel; James winds up Lauren by leaving a lamb chop in her bag.
- Rhiannon Jules and 22 members or associates of the AFA are brought to trial. Jules receives 18 years in prison; Mark, Adelaide and Viv receive 12 years and AFA member Jay Buckle (who helped James, Kyle and Tom infiltrate the depot) receives 9 years. Because of his youth and minimal role in Cobb's torture, Tom receives only four years. The two men who blinded Christine Pierce both receive seven years. Several other AFM members are also sentenced.
- Ryan Quinn leaves the Zebra Alliance after falling out with its leader, Madeline Laing. He then sets up his own animal rights organisation, Zebra 06.
- In late 2006, Malarek sells off it Corbyn Copse facility to a property developer and announces plan to wind down its operations over the next 18 months before building a new labratory in East Asia.
- Nick Cobb survives his injuries but suffers irreversible damage to his digestive system and requires several operations in the UK before recovering in a private Swiss clinic. His company, Cobb Cleanse Inc, settles out of court with the plaintiffs of the sink cleaner lawsuit, the parents of a toddler who accidentally drunk Cobb's sink cleaner, for an eight-figure sum.
- Mac officially retires on 28 July 2006, and celebrates with farewell drinks with a few senior staff members before leaving on a cruise with his wife.
Response to book
The cover of the book features a pair of eyes hidden beneath a balaclava. The balaclava has a white CHERUB logo printed on the centre of the forehead. If the cover of the book is looked at the other way up, the eyes of the person become angry. It is unsure as to whether this is deliberate or not.