Jennifer Peters (Justine Waddell) attempts to save her brother Roy, who has been abducted by a serial killer known as the Riddle Killer, or R.K, due to his use of riddles in the murders he commits. Jennifer has recently written a book about the nature of serial killers, to which R.K. has taken offense. Jennifer follows R.K.'s clues and finds Roy, but fails to save him as the car in which he is trapped explodes.
Kevin Parson (Marc Blucas) is a seminary theology student. Kevin has recently completed the third draft of his thesis about the nature of good and evil. One day, he receives a phone call from R.K. (Bill Moseley), demanding that he confess some unspecified sin, or his car will explode. He also tells Kevin a riddle: "What falls but never breaks? What breaks but never falls?" Puzzled at what sin he means and the riddle, Kevin quickly escapes from the car before the explosion. He informs the police, among them Jennifer, but leaves out the part about the sin the killer demanded he confess, believing that the sin is what he did some time ago.
Then he receives a threat against his childhood dog, and goes to the house of his Aunt Balinda (Priscilla Barnes). He fails to save his dog from a bomb. Back at his home, he meets up with his friend since childhood, Samantha Sheer (Laura Jordan). They decide to try to figure out the mystery of the Riddle Killer, who continues to target him, and who appears to be somehow able to monitor Kevin in his own home. Sam solves the first riddle, the answer is night and day. She is working as an insurance detective and takes the book in which the killer had hidden a mobile phone to the laboratory.
Then there is another threat from the Riddle Killer. A bomb is attached to Kevin's fellow student Henry and a message on Henry's forehead points to Romans 6:23, a bible text about death as the wages of sin. The police manages to get the bomb off Henry's body. Kevin now remembers a boy who had always watched him and Sam during their childhood. In self-defense, Kevin had locked him in a warehouse and left him to die. He thinks that the boy escaped, and is now R.K.
Later, Kevin finds the papers of his thesis scattered around his room. He finds a TV in his refrigerator which shows R.K. with another riddle, about something which takes you away, but does not go anywhere. Kevin confesses leaving the boy in the warehouse and apologizes, hoping to satisfy him and that he would now be left alone. However, R.K. insists that it is not sufficient and does not relent. Together with Sam, whose father worked as a policemen, he finds out that a bus on 3rd Avenue is in danger. He and Sam manage to get all the passengers off in time before a bomb explodes.
Jennifer visits Kevin's Aunt Balinda and finds that she has been keeping her husband and son Bobby in the dark about the entire world outside their home, and had done so to Kevin as well. She also finds a bloody jacket in the warehouse. In the meantime, Sam talks with Kevin, who is in a hotel now. R.K. sends a message on a tape to the hotel room which points to an empty building and the number 33369 - the warehouse. Before Jennifer gets to the hotel, Kevin and Sam are at the warehouse. There Sam sees a wall full of enigmatic words and then is trapped by the killer. When Kevin enters the building, he finds a bomb. He is unable to stop it, but can escape with Sam. Jennifer and the police arrive and investigate. Sam leaves, and Kevin insists on not cooperating with Jennifer, as the killer insisted on no police involvement, under threat of killing more people. Jennifer declares her resignation, saying that as she is no longer officially involved, she no longer counts. However, Kevin ignores her.
Kevin finds another threat about a house on a fire and midnight, realizing that his Aunt Belinda is in danger. He rushes to try to save her and remembers how his aunt had abused him when he was a child. Sam finds a note by R.K. and is startled to see he has the same handwriting as Kevin. She calls Jennifer, who tells her that there was only one pair of footprints in the warehouse. Sam is now sure that she had never actually seen R.K. The women also realize that all the riddles were about opposites, like nightfall and daybreak, and conclude that R.K. might actually be Kevin's "evil half."
Kevins finds Balinda tied up, and the Riddle Killer introduces himself as Slater (Bill Moseley). Sam rushes to Balinda's house, and finds that the Riddle Killer, Slater, is real after all when she looks under the door and sees two pairs of shoes. Slater explains that he will have Kevin kill Balinda, then leave him to take the blame, as everyone will believe Kevin is the Riddle Killer. Jennifer arrives to find Kevin pointing a gun at himself. As it turns out, Slater and Sam are both figments of Kevin's imagination. Kevin had been traumatized by the treatment by Balinda, had imagined his friend Samantha and the boy with whom he had fought, and had subconsciously imitated the real Riddle Killer. Jennifer convinces Kevin of this, and his visions of Slater and Sam vanish.
Kevin had said that the real Riddle Killer was right in front of their eyes, and Jennifer discovers while examining his wall of clippings that the hot dog vendor who had supposedly been given a book by the killer to give to her is at the front of the crowd in a photo, holding a camera. When captured, he confesses that he hates copycats and had meant to kill Kevin for copying him.
Kevin is sent to an institution, and Jennifer visits him there.
Rotten Tomatoes, a review aggregator, reports that 5% of 37 surveyed critics gave the film a positive review; the average rating is 3.3/10. The sites' consensus reads: "Thr3e is a shoddily made, thrill-free thriller that isn't half as good as the several movies it borrows from (Adaptation, Saw, Se7en)." The film also has a noticeable resemblance to the plot of a film script created by the character Donald Kaufmann in the movie Adaptation.
Rotten Tomatoes ranked Thr3e #84 on its "The 100 Worst Reviewed Films of All Time: 2000-2009" list
Three opened in just over 450 theaters and drew in US$700,000 its first weekend. The film had officially left the box office 17 days after it opened and grossed just over a million dollars.