Shirley Holmes investigates a string of suspicious fires, one of which took place in a shed at her school. The police believe that Bo Sawchuk, the school's newest student, a former gang member, is responsible for the arsons, but the young detective discovers that Bo's former associates are responsible for the fires as part of an insurance scam and framing the boy for the crimes.
Molly Hardy becomes Sussex Academy's newest student and immediately makes a splash by allowing a family heirloom, the ruby the King John wore when he signed the Magna Carta, to be displayed at the school. She joins Alecia's ticket to run for student counsel vice-president and other candidates drop out of the race due to a series of "accidents" making Molly the only viable choice for President. When the ring is stolen from it's display case, Shirley suspects Molly engineered to theft to gain sympathy and become a hero by framing another student for the "theft".
Shirley discovers an injured giant rabbit and returns the animal to its owner, the manager of a pet shop. She learns that the store has been broken into and tricks the victim into revealing that an illegal komodo dragon was among the animals stolen. Shirley and Bo trace the missing menagerie to a group of animal rights activists, one of whom was bitten by the poisonous reptile causing him to think he's the reincarnation of Noah.
Shirley finds Louisa, a frightened illegal alien from Central America, hiding in her school's laundry room. The young detective discovers that that a gang is importing the refugees into Canada to work as slave labor in sweatshops and one of the criminal leaders is a British diplomat who works at her father's embassy.
Intrigued by reports of alien abductions around her home, Shirley investigates and discovers that aliens had nothing to do with the abducting. After discovering mind-controlling implants placed in the victim's necks that cause the men to steal materials used to make explosives, she fears that the peace talks her father is brokering might be the target for the bombers.
When Bo starts to fall asleep in class, Shirley investigates and discovers that he's taken a second part-time job as a stable boy. During her visit to the racetrack, Shirley stumbles upon a plot to substitute a ringer for a perpetual back of the pack race horse, but is captured by the bad guys before she can alert the race officials to the crooked gambling scheme.
Stink tells his classmates a ghost story concerning a former Sussex Academy student who disappeared the night before an international piano recital and never seen again. According to Stink, the young woman's ghost can be heard crying in the attic on moonless nights. Molly Hardy, about to compete in the same event, dismisses the tale as pure fiction until she and her friends are confronted by ghostly music and nocturnal screams. When Molly goes missing, too, Shirley researches the events that occurred sixty years to go to see if there is a link between the ...
On his death bed, noted Egyptologist Sir Edward Stebbings gives Peggy Holmes an ancient toy and half a note written in hieroglyphics and tells her to piece it together with the other half of the message he gave her 40 years earlier. Sir Edward's sons are convinced that the completed message will reveal the whereabouts of Egyptian artifacts their father stole from pharaohs' tombs and hid in Canada. Shirley doesn't know what the old man's dying message meant, but decides to find out before the archaeologists' greedy children can lay their hands on whatever it may be.
Shirley and Bo become concerned when Ms. Stratmann, falls in love with the schoolmaster that Molly Hardy helped get fired from his position at another school. Molly, Shirley and Bo discover that Ms. Stratmann's suitor is a con man after her money, but the three disagree on how best to break up the romance before Ms. Stratmann is fleeced of her life savings.
Shirley is the only one concerned when Stink Patterson disappears from his own birthday party - his father even ignores repeated calls for a hefty, if unique ransom. Shirley and Bo finally convince the novelty store owner to take the theft seriously and manage to trail the villains to the hideout where Stink is held prisoner.
While attending a ceremony where the bones of Native-American warriors are re-interred, Shirley notices that one of the boxes of remains has been stolen. Undeterred by animals who seem intent upon disrupting her investigation, Shirley believes the trail of evidence points to a popular young man who was once a gang member.
When tabloid journalists link Robert Holmes with a lovely rock singer who's wanted for murder by the police, Shirley fears the worst. She manages to track the woman to an old fencing studio and learns that she's been framed for the bombing by the owner of a chain of health stores after she learned that the beverage the company is marketing causes dangerous side effects.
Concerned that Shirley still believes her mother is alive in Rawanda, Shirley's father insists that the girl detective visit a psychotherapist. In the waiting room, Shirley meets another uncomfortable patient, Rebecca Ratcliff. The actress begs off of her appointment because, after glancing at Shirley, she "remembers" an previous appointment with her mother in Rawanda. Intrigued, Shirley follows her to a nearby theater to find out what caused this remarkable outburst and is asked to appear in "A Midsummer's Night Dream" - a production that is dogged by unexplained ...