Jamal Jenkins' family is preparing for his older sister Danitra to go to college. That night Jamal sees strange things happening in the park, then receives a strange message on his computer from a mysterious being who asks, Where are the children? Are they all right? The next morning he revisits the park and finds a strange coded message, then finds a warning in his locker. His attempts to find out what's going on lead him to Lenni Frazier, a girl who lives with her musician father in an apartment above the bodega owned by the parents of Alex Fernandez and his little sister Gaby, who is the latest victim in a string of backpack thefts committed by unusual culprits. Lenni also receives a strange message in her notebook after speaking to Jamal. They find out they're the only ones who can see letters being rearranged on signs and posters, and decide to try and contact the mysterious spirit.

Jamal and Lenni find out their new friend can't see or hear, but can communicate through words, so they type to him on the computer. He doesn't know who he is or where he came from, but knows he used to be a man. They name him Ghostwriter, and try to crack the coded message Jamal found at the park, along with a button that says THABTO. Lenni has recommended Alex, who's an expert on mysteries and codes, so he goes to him. Gaby believes the stolen backpacks are being left in the junkyard, with only the lunch money missing from them. Alex and Jamal go with her.

Alex becomes a member of the Ghostwriter team. Jamal suspects THABTO is connected to the gang of people stealing backpacks, who wear green two-headed masks. The team asks Ghostwriter to find more THABTO buttons, and the search leads them to the Party Animal store where an order was placed for four buttons. Ghostwriter leads them to a locker at school that's connected to one of the THABTO members, but they don't know who. Gaby reveals she also got a coded message in her backpack, and the team now tries to crack two codes and decide to call on Ghostwriter for help.

Ghostwriter makes contact with Gaby, and she'd made a fourth member of the team. Alex finally catches somebody using the school locker Ghostwriter led them to, and follows the kid to the arcade where he joins three others who are playing a game called Double Defenders, about two-headed aliens. Alex finally figures out how to crack the coded message Jamal found, and they discover the THABTOs are meeting in the corner of the navy yard the night before the Double Defenders tournament for the final secret ceremony. Alex decides to infiltrate the THABTOs to find out what they're up to, and Lenni and Jamal work out a coded note to fool one member into not showing so Alex can fill his spot.

Alex gives the wrong name during the THABTO ceremony and is found out; he and his friends are chased through the navy yard by the three remaining members. They manage to escape and regroup to figure out the THABTOs' plan. Going over the tape recording of the THABTOs' ceremony, they decipher the group's chant to figure out their plan for the Double Defenders tournament.

Jamal is playing a computer game inside Mr. Brinker's video store, when a man comes in and gives Mr. Brinker a piece of paper that enrages him. Tina comes in to buy a blank videotape, but insists the one Brinker hands her isn't new, he yells at her and runs her out, then yells at Jamal, complaining about kids running off his customers and only buying cheap things. Jamal goes home and writes a complaint letter against Mr. Brinker. He goes back to the store at 7 P.M. and drops it in the slot in the door, then firecrackers go off behind him, and he rips his sleeve in the door slot. After Jamal leaves a fire breaks out in the back room. The next morning Ghostwriter sends Alex, Gaby and Lenni a message to get to Brinker's store, where the police are investigating the cause of the fire. Lenni picks up Jamal's letter without realizing what it is. Meanwhile, Jamal tries to help Craig, the new kid, get in a game of basketball against Momo to see who's the better player.