Luke McNamara (Joshua Jackson) is college senior from a working class background with the aspirations to become a lawyer. He attends college along with his quasi-girlfriend Chloe (Leslie Bibb) and his best friend Will (Hill Harper), working to pay for his education. Even if he has good grades and he’s captain of the school’s championship varsity crew team, Luke knows it will take much more to secure a spot in a top law school. At the opposite, Caleb Mandrake (Paul Walker) is the rich, arrogant, selfish son of the powerful Judge Litten Mandrake (Craig T. Nelson). They are both call in the night, for entry into the highly selective secret society known as The Skulls. Luke jumps at the chance, hoping it will help to guarantee him both the financial means and the connections to make it into law school. Caleb was fated to become a skulls since he’s born, his father his one of the highest members on The Skulls council.
As part of his initiation, the members of the senior class who have been tapped for admission must partake in a series of traditional rituals to test their loyalty, honesty and strength of character. Those who succeed will be rewarded with brotherhood, influence and money. The first test is to steal the symbol of another Society. Thanks to the courage and the initiative of Caleb and Luke, they’re all admitted in the The Skulls.

But not everyone shares Luke’s rosy view of the organization, Luke's friendships with Will hit the rocks. Even Chloe is torn. She thinks he may be too good, too firm in his populist goodwill to join a restrictive, elitist group dedicated to propagating their own agendas. As a member of the skulls, Luke is partnered with Caleb to be “soulmates” . For Caleb, Luke possesses everything he lacks—self-reliance, ambition and drive. And in Caleb, Luke has a clear view of everything he aspires to—wealth, sophistication and prestige. As a Skull initiate, Luke is invited to be a part of the Mandrake family’s holiday gatherings, creating a stronger bond between him and his soulmate and he meets Mandrake’s soulmate Senator Ames Levritt (William L. Petersen). But behind the Mandrake family facade there is unease. In private, Judge Mandrake treats his son harshly, disappointed in his lack of ambition and pride in his lineage. Caleb finds his father’s disapproval unbearable, though he does his best to conceal it.

When Will commits suicide under suspicious circumstances, Luke, deeply troubled by the death of his best friend, becomes suspicious of what actually happened to him, and is forced to confront the possibility that he was murdered for attempting to reveal the secrets of The Skulls. Will, unbeknownst to Luke, was writing an exposé of their prized secret rituals. During another ritual, Luke ask to Caleb to tell him the truth about Will’s death. Caleb admits that Will stole the key of the secret’s ritual room and his book from his car. He caughts Will taking photos in the ritual room and in the ensuing struggle Will’s fall. Caleb assumed that Will was dead when he left the room.

With the advice of Sen. Levritt, and the help of some of his old townie friends, Luke obtains tapes that prove that Mr. Mandrake's hitman committed the murder - not Caleb. The tape’s showing Will unconscious, but still alive. Caleb was ordered to leave the room by his father, after which the Dean Martin Lombard (Christopher McDonald) breaks Will's neck. The skulls manage to move the body and make it look like Will committed suicide.

Before Luke can show the evidence to police, the tape is switched by the local detective, maybe controlled bu the Skulls too, and Luke ends up being confined to a mental hospital.

Meanwhile, Chloe reveal to Caleb the truth about Will's death, but he just can’t belive it. With the help of Sen.Levritt and Chloe, Luke manages to escape the mental hospital. Dean Lombard run after Like and Chloe, but they are saved by the same police man who swithced the tape, who’s in fact working for Sen. Levritt. Luke knows that his only option is to fight The Skulls by their own rules. He challenges Caleb to a duel at The Skulls' private island. Caleb's father tries to take his son's place in the duel, but is denied the opportunity due to another Skull rule. After the two college students take their paces and turn around, Luke drops his gun and tries to convince Caleb of the truth, being that he is not responsible for Will's murder.Despite being pressured by his father to kill Luke, Caleb cannot bring himself to pull the trigger. At this point, Caleb's father loses control, grabs a pistol, and attempts to shoot Luke himself.

The movie was filmed at the University of Toronto but it is strongly hinted that the plot takes place at Yale, with large "Y"s on uniforms and walls the most prominent clue. Also, during a scene in a bar, the rowers are seen singing "Mory's Song," a traditional Yale song of celebration. Many of U of T's most notable buildings are featured in the film. A part of University College stands in for the Skull's headquarters while the office of the Skull's evil leader shown as being in Trinity College. The rival society is headquartered in the student council building. The protagonists live and eat in Burwash Hall. The opening rowing scene was shot in St. Catharines, Ontario.

The film features both William Petersen and Hill Harper. Harper is currently a star of CSI: NY, the spin-off of Petersen's series CSI: Crime Scene Investigation.

The Skull-and-Bones Society (on which this movie was based) actually gives out watches to each class of skulls, though not necessarily with the whole branding ceremony. After the movie was filmed, Joshua Jackson acquired one of the actual watches and gave it to director Rob Cohen.

Yale is never mentioned by name during the film, but there are plenty of references:

At the boat race, every team is mentioned by its school name, except for "The Bulldogs." (They're the Yale team.)

The characters wear Ys on their sports uniforms.

The Skulls are said to have "322 alumni worldwide." The Yale secret society Skull & Bones uses the number 322 as an identifier on many of its symbols.

The characters are seen celebrating at a pizza parlor they refer to as "Mory's," drinking from a big golden cup. Mory's is an actual place, and the tradition with the song and the big golden cup is accurate; however, it's a formal restaurant, not a pizza parlor.

The new Skulls are sent to raid "Snake & Skeleton." There is a Yale secret society called "Book & Snake."

Some campus shots seem to purposefully mimic Yale buildings. There's a tower that looks a lot like Harkness Tower, and the dining hall looks like the one at Berkeley College.

The wristwatch that each new member of the Skulls is given is the Breitling Old Navitimer.

At the university (actually the University of Toronto), you can see the lights for the Sutton Hotel in the background (red lettering) in downtown Toronto, Ontario, Canada.

Director Rob Cohen make a cameo as the professor of Joshua Jackson''s character.

Paul’s father, Paul Walker III, take the role of Caleb’s boxing coach.

In the motel scene, the lead characters are drinking from "Coffee Bean and Tea Leaf" cups. However, there are no branches of this coffee chain anywhere in the northeast United States or Canada (at time of filming).

Hill Harper's character, Will, who plays Luke's roommate in the film, is modeled after director Rob Cohen's real life Harvard roommate.