Melanie St. John, an old friend of Zoey's is suspected of murdering her estranged husband Robert. Zoe and Dan are assigned to work on the case and find that there are many more suspects including a son-in-law who had a suspicious relationship with his father. Zoe and Dan are sprayed with a fire extinguisher when they interrupt a burglary in progress at Robert's house. Taylor gets a job as a waitress in a mama and papa restaurant and begins flirting with a waiter who also works there.

A kidney is stolen from a nurse on an elevator who is delivering it for a surgery. While searching for the kidney, Zoe and Dan try to expose a man they suspect of faking disabilities. Zoey's car is stolen with Hannah's volcano science project in it! Zoey must get her car back with Hannah's volcano before Hannah finds out it is missing as well as find the kidney and save the patient's life.

M's ex-husband Graham decides to run for mayor and Taylor decides to work on his campaign team. At a campaign rally, a bullet that evidently was intended for him hits Taylor's friend and she is rushed to a hospital. Due to some excellent ""Zoeyism"", a secret affair and the many clues required to figure out who is behind the attempted murder are found. Also, Dan is concerned when he suspects a campaign worker of flirting with Taylor.

Zoey finds out that her boyfriend is married and angrily breaks up with him. The next day he is found murdered and Zoe is suspected of murdering him! Zoey finds out from her bank that her identity has been stolen by a woman resembling her who has been using Zoe's name. Taylor, Cliff, and Hannah are delighted when a large expensive boat is delivered to their house while Taylor is furthur excited when Dan buys an expensive lightbulb for her fundraiser.

Zoe and M attend a fashion show. Zoey witnesses a famous designer being kidnapped. There is no shortage of suspects from a cheating wife to a rival designer. When the ransom money is captured by the kidnapper, Zoe and Dan must find the designer and get M's money back or they could lose their jobs! Also, Taylor, Cliff, and Hannah are forced to give their messy house an extreme makeover and face some difficulties.

Dan goes a bit too undercover when he is assigned to find out when and where upcoming jewelry robberies are to take place. Small-time robber Carmen romances Dan while Zoey and M begin to wonder if he is purposely misleading them and returning to his criminal past when a robbery takes place at a different jewelry store than the one he told them it would. Zoey is annoyed by an unattractive man at a bar. Taylor and Zoey are in serious trouble when a friend of Taylor's who is illegally enrolled in Taylor's high school under their address gets in a fight with another boy who sues him.

A man who narrowly misses getting hit by a bus suddenly realizes that he has no idea where he is and who he is. He hires Zoe and Dan to find out his identity. After narrowly escaping severe injury or death several more times, Zoe and Dan are convinced a hit man is after the man; who is convinced that his name is Brad Pitt and that he has a sister named Mary. Amazingly, Zoe and Dan are able to locate his girlfriend, who is very upset at him for some reason. They must convince the angry woman to reveal his identity. Meanwhile, Hannah practices for a flute recital and M., Zoe, and Dan are annoyed by a new tenant in their office building.

Zoey and Dan try to find out if a medical researcher who was locked in a room filled with hydrogen gas was murdered or if the incident was an accident. A psychic who claims to be receiving messages helps them and eerily is able to give them clues to the mystery. Meanwhile, Zoey bids on a silver dollar on an online auction and is frustrated when another bidder keeps topping her bids. Also, Hannah asks the psychic if she can talk to her mom.

The wife of a mob boss hires Zoe to find her daughter. An overprotective police officer refuses to let them see the case files so they seek professional help. Dan goes undercover and faces some difficulties. The team is threatened by the mob boss to back off the case. They learn that the girl may not really be missing and that some people may be lying. Meanwhile, Dan tries to help Cliff become less arrogant and delusional after he flirts with one of his teachers.

A mystery author murders her greedy cousin. Then she hires M., Zoe, & Dan to prove that his death (which is assumed to be suicide) was murder. Greedy relatives wishing to inherit are murdered one by one and the writer frames a likely suspect. Meanwhile, Hannah (with the help of Taylor and Cliff) avoids going to her "Firefly" sessions.

A blind radio star with strong opinions about politics and corruption is attacked while he is on the air. Zoe, Dan, & M. figure out that he is being attacked because he is accusing a large company of corrupting its employees. When a witness is in a terrible accident, the detectives know that something must be done! Meanwhile, Cliff makes a video documentary of Zoey.

When Zoe and Dan are left stranded on a bridge when Dan's convertible runs out of gas, a woman hands them a baby and jumps off the bridge. Zoe and Dan grow attached to the baby and are determined to figure out what caused the mother to jump to her death. Her fiance reveals that she was a mail-order bride and Zoe and Dan go undercover to investigate the shocking world of wives for sale.

As Zoe, Dan, M., and their co-workers get ready to leave work for the day, a woman gets off the elevator on their floor and holds them hostage at gunpoint. Zoe recognizes her as the mother of a recently convicted murderer whom the team had helped convict. The woman reveals that somebody at M. Pearl McGuire Investigations contacted her claiming to have evidence that would prove her son was innocent and that she was supposed to bring $25,000 to buy the evidence. M. is determined to find the blackmailer and nobody is above suspicion! Meanwhile, M. is nominated for Businessperson of the Year and Dan's father comes for a visit while back at the Busiek house, Hannah has a friend over while Taylor works on a paper with a boy who has a bad reputation.

As the anniversary of Zoe's sister's death grows nears, Zoe begins seeing her sister and talking to her while remembering the good and the bad times they had together while helping Taylor and Hannah cope with the painful time. Meanwhile, Zoe, Dan, and M. investigate a robbery at a fertility clinic and must work with a flighty and not-so-helpful witness to catch the thief.

Zoe's ex-boyfriend from Las Vegas, a famous piano player, shows up in Chicago and asks her to find a "thief" who's been breaking into his house and giving him half-eaten sandwiches and clothes. Meanwhile, a greedy lawyer falls through a window while showing off his bravery to potential employees. When a video camera reveals that Zoe's ex-boyfriend was on the same floor as the lawyer that same day, she must find out if he has anything to do with the apparent accident.

Zoey has back problems and M. insists that she goes to see her chiropractor. Once there, she's attended to by an attractive doctor around her age and the two hit it off. Dan, meanwhile, must work with a bounty hunter to locate a man who viciously murdered his wife and her attraction to him isn't reciprocated.

In the series finale, Zoe and Dan go undercover as a soon-to-be-married couple to catch Leo's sister's murderer, who is a wedding planner. As they struggle to keep their cover, Zoe discovers an offensive item in Dan's suitcase and nearly calls off the "wedding". Meanwhile, Leo isn't afraid to break the rules to nab the killer. Taylor, Hannah, and Cliff are convinced that Zoe has eloped with Dan when they overhear a phone conversation. In the end, an emotional wedding leaves Zoe and Dan in a sticky situtation.