A Few Good Men begins with two marine officers, Harold Dawson and Louden Downey, charged with the murder of a fellow officer, William Santiago. William’s body was found with a rag jammed in his mouth. The cause of death was suffocation due to an unknown medical condition that accelerated his suffocation when a rag was jammed into his mouth. Daniel Kaffee, an unenthusiastic military lawyer, is assigned the case by the military court. He initially draws up a quick plea deal for Harold a Louden, but they refuse and uphold their innocence. Daniel and another lawyer Galloway travel to where the murder took place in Cuba at the Guantanamo Bay Navy Base to question the officers present during the crime. Initially, it's believed that Harold and Louden were ordered to carry out a “Code Red” (an illegal extrajudicial punishment gone wrong) by their commanding officer Jonathan Kendrick.
While questioning officers at the base, Daniel discovers that William was not very popular at the base as he often broke the chain of command and was greatly disliked by many officers. He also discovers that William has put in a request to be transferred to a different base altogether. The commander of the base Nathan Jessup lies when being questioned about William claiming that he ordered his transfer when in fact he never ordered it until after his death to cover up the fact. It is also revealed that Jonathan had ordered that no harm was to come to William for his decision to leave the base when in fact he secretly ordered a code red on him. All these facts are uncovered by Colonel Matthew Markinson who had initially advocated for William’s release but failed.
The case becomes a matter for the military court when these facts are uncovered. After further investigations, Louden confesses that he did not receive the code red order directly from their commanding officer and that Harold was the only one to receive those orders. Louden was enlisted by Harold to assist him in the extrajudicial punishment that turned into a murder. To win this case, Daniel has to arraign his witness Matthew who could confirm the allegations in front of the court. Matthew commits suicide for fear of testifying against his fellow officers.
Daniel has no choice but to call Nathan Jessup to the stand as a witness. This bold move runs the risk of getting Daniel arraigned in court for disrespecting an officer of a higher ranking. Daniel, however, has a plan to get Nathan to confess to the crime unknowingly. Daniel uses the fact that he lied during his initial questioning about William’s request for transfer. Caught in his lie in front of the court, Nathan loses his composure and begins to rant uncontrollably further incriminating himself and his second in command Kendrick. Nathan is placed under arrest and Jonathan Kendrick is later arrested. Harold and Louden are acquitted of murder charges but are found unfit for military service. They are discharged dishonorably.