After a break-in at the San Francisco headquarters of a company, the police are called in. One of the executives has been murdered, and the security guard has been bludgeoned. It is not a simple robbery, as the executive was killed by shots from two different guns, nothing was stolen, and there are several other unexplained facts. Virgil Tibbs is contacted by the group which committed the break-in and stole four million dollars' worth of heroin. They are urban revolutionaries who explain that the company is a front for drug-dealing. They had hoped the break-in would lead the police to investigate the company itself and want to use the heroin to get to the leaders of the organization. Tibbs arrests the security guard to question him, but the guard is murdered while sitting in the police car. Tibbs agrees to help the group if they co-operate with him. One member of the group is hunted down and beaten by the drug pushers and another is murdered. Tibbs himself comes under suspicion from his superiors when the narcotics division tie him to the stolen drugs, whereupon he is removed from the case and suspended. He persuades one of his colleagues to help him with information on the bogus company behind the drug traffic. One of the revolutionaries, Juan, contacts the drug dealers and offers them the drugs back for $500,000. He sets it up smartly, proposing to exchange the first half of the drugs for half the money, using identical suitcases in a very busy square. Once the exchange takes place one of the other revolutionaries 'robs' the suitcase containing the money. The drug dealer shoots a policeman and tries to get away but is tackled by Juan and arrested. Juan notes the license plate on the car of the criminal executive who had come to supervise the deal. The revolutionary escapes with money, pursued by some of the gang through the construction site for the unfinished Montgomery Street Station. Tibbs goes to the house of the wife of the security guard. When Tibbs' colleague arrives, Tibbs confronts the wife, accuses her of being a runner for the gang, shows heroin in a package she has just brought home, and tells her she can choose between prison or being killed by the mob like her husband. She gives in and identifies the two chiefs of the organization. The chiefs are arrested by a large group of police officers, including Tibbs. When they are taken to the police car, a mob hit-man takes them out before they can talk. Tibbs now sees that he won a battle but is losing a war.
The film received largely poor reviews from critics, with Roger Ebert giving it a two-star review and stating that "the plot is not exactly believable", while A.H. Weiler in The New York Times wrote "The Organization can be rough on super-city sleuths as well as movie-goers who've been through much the same melodramatics before".
