Shirley and her friends pit knowledge against witchcraft when the school librarian, a devotee of Wicca, attempts to use her knowledge of black magic to capture Mr. Howie's affections, injure Ms. Stratmann and cast spells on the children.
Stink asks Shirley to help prove his dog, Barf, is innocent of the crimes the city dog catcher has accused him of - namely, eating seven of his neighbor's cats. Shirley becomes convinced Barf has been framed when she learns that all of the missing cats were either black or white - and dogs are color-blind.
While shopping in the mall, Shirley has her backpack full of tools stolen by a pair of diminutive thieves. Determined to get her gear back, she traces the pair to an abandoned house and learns that an old boy is using children to steal for him. In order to break up the gang without causing the children harm, Shirley decides to go infiltrate the gang and gains admittance by stealing a police detective's personal car.
Mr. Howie discovers a baby has been left on his doorstep overnight with a message warning him not to call the police. Not knowing what else to do, the history teach brings the child to school with him, where Shirley and Bo stumble on his secret. Shirley agrees to help Mr. Howie by locating the baby's parents and she follows the clues to a small circus operating downtown.
Shirley becomes intensely jealous of the attention Bo is lavishing on a pretty new student. The young detective's interest is piqued by the new girl's vocabulary which points to a British rather than an American background. Her attempts to pry into her rival's past blow the girl's cover and set a pair of assassins on the princess' trail.
Shirley is intrigued by a series of accidents that suddenly plague a long-running live children's television program and decides to investigate. Her suspects include the show's disgruntled second banana, the writers who want to replace the show's puppets with computerized animals and a producer who is under the gun to pump up the show's ratings.
Sussex Academy is thrown into a panic when a mysterious monster is spotted in the toilets, the shower room, the kitchen and the sewer. When a large sea serpent is observed swimming in the nearby Reddington River, Shirley decides that the smaller critter must be a baby trapped somehow in the private school's pipes. She and her friends attempt to help the baby creature return to its mother before unscrupulous entrepreneurs can capture it and put it on display.
While cutting the grass for an eccentric woman, Bo overhears the woman's son, just recently returning to the city, ask where the 500,000 was hidden. Since the woman doesn't know, Bo enlists Shirley's help to find the hidden cash. Shirley soon discovers that the treasure she's searching for is stolen diamonds from a jewelry heist more than 15 years ago and she's in a race with an ex-con to recover the loot.
Bart James's 12th birthday party is a big success when he and his friends are visited by a poltergeist. Bart believes that they have met the manifestation of his family's gardener who was fired during the 1930s, but Shirley wonders if the phantom may not be the spirit of a spinster who was boarding with the James's at that time and who disappeared, never to be seen again.
When an embassy decoding card disappear from Robert Holmes's safe, counterespionage officials consider him complicit in the theft. Shirley naturally believes her father is innocent and sets about finding the real thief. She is perplexed when an intruder subsequently breaks into their home and leaves a dead bird on her bed, takes a sheet and lays it on an outdoor doll house and then steals an antique dagger. With Bo's help, Shirley tries to discover what connect these strange incidents have with the theft of the top-secret code.
A Sussex Academy camping trip takes a disastrous turn when the lead character in Stink's ghost story about the hook-handed pirate who founded Reddington is all too corporeal. The children scatter into the woods - Shirley and Bart to track the nocturnal menace, Molly to complete an orienteering course so she can qualify for the world championships, Stink to scare Molly and Bo and Alicia to scare Stink. Will any of them survive to camp another night?
An African man suffering from amnesia delivers Joanna Holmes' stethoscope to Robert and Shirley. Despite her father's explicit orders not to talk to the man, Shirley and Bo track him to a squatter's shack in the middle of the park. Though the man's memory still fails him, Bo traces him to a nearby Catholic church where he learns the man served as a priest. From the African's robes, Shirley discovers the man has been using an assumed identity after fleeing from Rawanda. When her father learns of Shirley's efforts despite his instructions, he grounds the girl detective,...
Bo's cousin Zack is the lead singer for "Oath", the hottest new band in Reddington. In the past two weeks, they've scored numerous gigs, arranged for a television appearance and signed a record deal. Shirley likes Zack and loves his music, but can't shake the feeling that someone is sabotaging other bands to clear the way for Oath's rapid ascent to stardom.
When Shirley's television reception is disrupted during an interview with her father, she compares notes with Alicia and Bo and discovers both their households had similar interference. When Bart declines any information, Shirley presses him and learns that the static was caused when Bart tried to replicate a communication with extraterrestrial beings that he had overheard at the SETI (Search for Extra-Terrestrial Intelligence) outpost from which he had been inexplicably fired. Shirley and Bo agree to help Bart get to the bottom of the mystery.
Mr. Howie stays at the Howie Farm, but when he stays their longer than he had expected, Shirley has questions. Not only do the animals on the farm act nuts, but there is a ghost legend, and a feud between the Howies and the Wilkinsons.