Jamal releases Ghostwriter while cleaning the basement. Jamal, Alex, Lenni, and Gaby come together through the bond of Ghostwriter's mysterious messages to them all. They all come together to solve a rash of mysterious backpack thefts and their connection to a group of gamers calling themselves the THABTOs, an acronym for Two Heads Are Better Than One.

Guest stars: Samuel L. Jackson as Jamal's dad, Wil Horneff as Calvin Ferguson, and Mark Linn-Baker as the policeman

• Notes:
  • This story arc and 'To the Light' are the only stories to have five episodes. The rest all conclude in four.
  • This story arc is not the original pilot. The next arc, 'Who Burned Mr. Brinker's Store?', was produced first and was intended to be the pilot for the series. However, wanting a better introduction to the series, the producers decided to add "Ghost Story" at the last minute.
  • One of four story arcs to be adapted into a book.

Jamal is angered when Mr. Brinker (Max Wright), owner of the privately own video rental shop, yells at him. But that night, when Brinker's store burns down, the shopkeeper accuses Jamal of arson to cover up his own involvement in the fire, which itself was a cover for a much more serious crime that he committed. Ghostwriter reveals himself to both Craig and Tina.

Guest stars: Samuel L. Jackson as Jamal's dad, Jeremy Miller as Craig, and Lou Albano as the taxi driver interviewed by Gaby and Tina

• Notes:
  • This story arc was the original pilot. This is evident from the fact that this arc seems to have been filmed inside actual buildings and houses, instead of on a soundstage like the rest of the series. Other indications include Ghostwriter appearing as a plain star instead of the trademark logo and using only the word RALLY without an initial when calling for a group meeting. Also, the main cast members appear much younger than they did in "Ghost Story".
  • Craig does not appear again in the series and is never referred to again. It is unknown whether it had anything to do with this being the pilot episode.
  • Lieutenant Isaiah McQuade makes his first appearance as a recurring character. Although he introduced himself as working for the Arsons and Explosives Division of an NYPD precinct, he later gets called by the team to help investigate other kinds of crimes.

Alex has aspirations to become class president, but one of his competitors starts a smear campaign, putting up fliers with embarrassing personal secrets. One of the initial suspects is new transfer student Rob, because of his withdrawn nature, but that status changes once Ghostwriter reveals himself to him. Eventually Alex realizes that one of his many pen pals might be involved in the dirty politics, and might be leaking info to the real dirty politician, Calvin Ferguson (Joey Shea), whose main goal is to keep Alex from winning.

Guest star: Ellen Foley makes her first appearance as Ms. Kelly, Dulé Hill appears as a basketball player during two episodes,

• Notes:
  • Rob joins the cast in this story arc.
  • Wil Horneff who previously played Calvin Ferguson in the story arc "Ghost Story", is replaced by Joey Shea beginning with this story arc.

Lenni persuades the team to enter a scavenger hunt-style contest in order to win the chance to be drawn into an issue of Hoodman. Their efforts are hindered by an embittered comic book artist named Manny Gites (Mike Jefferson), who will stop at nothing to win the contest disguised as his own character, Stoop Dude. Meanwhile, Rob continues to be distant from the team, but makes friends with an eccentric homeless poet.

Rob takes Jamal to meet Double-T, but they find his usual spot trashed and the poet missing. After tracking down Double-T's daughter Lisa (Kristy Graves), she and Rob trace his usual hangouts, but wind up trapped in a subway cave-in. Rob relies on his wits and Ghostwriter to try to get help and continue the hunt for Double-T, while the rest of the team use some of Double T's poems and learn of his service in the Vietnam War, to assist in the search.

• Note: This story arc and "Ghost Story" are the only stories to have five episodes. The remaining arcs in the series all conclude in four.

The team is hard at work at the community garden center when a series of health problems arise: Gaby passes out, several other kids and adults get sick, and even some rabbits die. It's soon learned that a highly toxic chemical, tetrachloroethylene (commonly known as "perc") has been illegally dumped in the ground under the garden and is to blame. As the authorities cannot remove the barrels in a reasonable amount of time, unless the guilty party is tracked down, the team sets off to find the person responsible for such a dirty act. Investigation eventually leads to a local philanthropist named John Miller (Brian Reddy), who may not be the "Citizen of the Year" that he seems.

Plans for the school's talent show are threatened when a gang moves into the neighborhood. Kids start coming to school with black eyes and bandages, and then the school's hallway gets tagged by graffiti artists. Rob's new friend, Victor Torres, a former member of the gang who had quit after his brother became permanently disabled after a gang war, appears to be the prime suspect, but Rob is determined to prove that someone is out to frame Victor. Someone in the school named Tony Boyd (Greg Young) holds a personal grudge against him.

Galaxy Girl, Gaby's favorite action hero, is coming to town, and Gaby "borrows" some money from her parents' bodega to buy a costume. When she learns she cannot return it, she realizes she must fess up. She gets into more hot water when a valuable model spaceship from the show is stolen and winds up in her room. Someone is framing Gaby, but who? And why? Somehow the whole story arc may just be a fancy game of hyperball, the infamous Galaxy Girl game, initiated by someone who is determined to teach the producer of "Galaxy Girl" a lesson.

The Ghostwriter team begins to fall apart when arguments and misunderstandings stemming from a car accident between Mr. Fernandez and Mr. Frazier start to form between the team members. Lenni sides with her father, and Alex and Gaby side with their father. Tina is also involved because she had witnessed the accident and had unintentionally provided testimony against Mr. Fernandez to the press. While Jamal tries to ease increasing tensions, Rob withdraws, unable to handle the fighting. The rift starts to make Ghostwriter fade away, and Calvin Ferguson makes things worse by trying to investigate who 'GW' is (he caught Rob talking to "GW" in school) and makes attempts to further sabotage the team. Rob eventually helps Jamal get the team back together in time to solve the mystery of an art thief, as the culprit Daniel O'Connor (Jonathan Salinger) may also be indirectly responsible for the car accident. The story arc ends with an unknown hand writing a distress call, causing Ghostwriter to abruptly leave the team.

Guest star: Bo Jackson as Joe, the security guard

• Note: This is the only story arc to end with a cliffhanger into the next one.

The hand writing the distress call to Ghostwriter belongs to Frank Flynn, a boy who lived in Jamal's house in 1928. Ghostwriter's strength is pushed to its limits when he has to time travel from Frank and his best friend Catherine in 1928, to Jamal and the team in 1993, and back, in order to help Frank clear his name in the theft of a priceless tea set, as if he is not cleared, he will be sent to live in an orphanage. Meanwhile, Jamal learns his dad is getting very sick, and clearing Frank's name may be the only link to his recovery, as he played an important role in Jamal's father's childhood.

Guest stars: Louis Tadaro as Frank, Grace Johnston as Catherine Canellan, Stephi Lineburg as Lucy Canellan, Cynthia Crumlish as Mrs. O'Boyle, Thomas Schall as Dr. Canellan, William Hill as Raynard Wilcox, Charles Mann as Mr. Izzo, Augusta Dabney as Catherine Canellan-Flynn, and Laurie Klatscher as the librarian

• Notes:
  • Ghostwriter reveals himself to Frank, Catherine, and Lucy in this story arc.
  • Catherine Canellan-Flynn is the only adult ever to see Ghostwriter during the series.
  • Although credited, Rob does not appear in this story arc.
  • One of four story arcs to be adapted into a book. The episode takes place in 1993, the original air date. The book adaptation's current time is 1996, the year it was published.

Tina befriends a foreign exchange student, Safira (Madala Hilaire), from Mozambique, whose father is an important ambassador. Their family has had a serious rift, and her brother fled to America after an argument with their dad. Safira intends to find her brother, having written letters to each other since he fled. But, in her search, she herself becomes lost and in a dangerous position. Meanwhile, Rob learns he has to move to Australia. Alex's new friend Hector (William Hernandez) meets Ghostwriter and goes on to take Rob's place on the team.

Guest stars: Cathy Rigby as Mrs. Dozier and K. Todd Freeman as Malenga

• Notes:
  • Ghostwriter reveals himself to Hector in this story arc.
  • Rob leaves the series and Hector joins the cast in this arc.

A hacker who goes by the name Max Mouse online invades Hurston School's computer mainframe, causing frequent fire drills, threatening messages, and altering the grades of Jamal and Lenni. The team gets a 'crash' course in the Internet in its cruder and more basic form, including chat rooms and bulletin boards, sending Ghostwriter through the computer and phone lines in an attempt to catch Max Mouse and stop his reign of mischief, as well as catch the student Janice Hall (Danielle McGovern) responsible for infecting the system.

Lenni gets the chance of a lifetime when a hip music producer wants to sign her to the Smash Records label and produce a music video for MTV. Lenni struggles to come up with an original song, but then nails one out of the park with a song called "You Gotta Believe". Lenni and the entire Ghostwriter Team get to go on-set for the filming of the video, but a series of strange accidents happen. It turns out that the target is not Lenni, but Jade, her producer. The team wrestles with the mystery of the accidents, as well as trying to babysit Jamal's cousin, Casey (Lateaka Vinson), who ends up meeting Ghostwriter.

Guest stars: Robin Leach as Marlon Campbell, Annabelle Gurwitch as Jade Morgan, and Mia Korf as Sonia, as well as cameos from hip hop trio Salt-N-Pepa and MTV VJs Doctor Dré and Ed Lover. Victor Sierra also reprises his role as Victor Torres, and Dennis Starolselsky as Kevin and Oren Sofer as Spencer make cameos to foreshadow the next story arc.

• Notes:
  • Ghostwriter reveals himself to Casey and she joins the cast in this story arc.
  • Richard Cox, who previously played the role of Max Frazier, Lenni's dad, is replaced by Keith Langsdale beginning with this story arc.

Alex becomes detached and moody with Gaby and the team, upon joining the three-man basketball team the Dragons. Also, a series of drug-related locker break-ins make them worry Alex may be involved with drugs.

Guest stars: Victor Sierra reprises his role as Victor Torres. Dennis Starolselsky as Kevin, Oren Sofer as Spencer, Elan Rivera as Maria, Julia Jordan as Delilah, Jesse Moore as Mr. Johnson, Patricia Maurceri as Mrs. Michaels, Mike Starr as Big Ralph, Kelly Kristjanson as Mary Jo, Jesse Tendler as Arnie, Z. Wright as Jason, and Damien Leake as Mr. Oliver

• Notes:
  • This story arc aired both on PBS and in broadcast syndication with a preface read out by the actors portraying Gaby (Mayteana Morales) and Mr. Fernandez (Shawn Elliott) before the start of each part.
  • Cordelia González, who previously played the role of Estella Fernandez, Alex and Gaby's mom, is replaced by Iliana Guibert in this story arc.

Katie Couric visits the set of Ghostwriter and interviews Blaze Berdahl (Lenni) and Sheldon Turnpiseed (Jamal), discussing the storylines for the forthcoming third season, as well as showing clips of the new episodes, screen tests and bloopers. Couric also has an interview with Melissa González, the new actress playing Gaby in season 3.

• Note: Most PBS stations aired the special the week before or the week of pledge drive time, when the stations normally pre-empted Ghostwriter for two weeks.

Jamal is vacationing in London with his parents and they are staying in the bed and breakfast owned by the Wentwood family. While there, Jamal befriends the Wentwoods' children, Sam and Becky. Using Ghostwriter to send messages back and forth across the Atlantic Ocean, they work together with the rest of the team to uncover a plot to kidnap the son of a famous author.

Guest stars: Andrew Cassidy as Sam, Candace Hallinan as Becky, and Julia Stiles as Erica Dansby, as well as cameos by Ahmad Rashad, Phylicia Rashad and Condola Rashad.

• Notes:
  • Ghostwriter reveals himself to Sam and Becky.
  • This is Mayteana Morales' last story arc playing Gaby.
  • One of four stories to be adapted into a book.

Gaby discovers a rare bird not realizing that it is sought by smugglers, taxidermist Aubodon Poulet (Kevin Chamberlin) and his assistant Honey Hawke (Alyson Reed) determined to claim the bird as their latest taxidermy prize.

• Note: Melissa González portrays Gaby beginning with this story arc.

The team helps Casey write her own story for a contest revolving around the "Gooey Gus" doll.

• Note: One of four story arcs to be adapted into a book.