In this case, the injustice may lie not in the conviction, but in the failure to negotiate the charges. The unstructured presentation of the facts in “Serial” obscured a strong case for the prosecution. A former classmate who was cross-examined for five days testified that Mr. Syed confessed to the killing, as he enlisted his help in burying the body. On the evening of Ms. Lee’s disappearance, Mr. Syed’s cellphone pinged cell towers near the burial site. A bargaining effort should have been undertaken here.

First-degree murder under Maryland law, for a case like Mr. Syed’s, requires that a killing be premeditated or the result of the commission of a felony. The prosecution’s theory was that Mr. Syed strangled Ms. Lee in a 21-minute car-ride after school. Strangulation, however, is not typically associated with premeditation, and the robbery, kidnapping and false imprisonment charges Mr. Syed also faced appear strained. The former classmate’s reliability was compromised, and the cellphone evidence was open to interpretation.

In addition, there was the mitigating factor of Mr. Syed’s age at the time of the crime. Seventeen is an age of increased inclination to take risks and limited impulse control. Age, as the juvenile justice scholar Barry Feld notes, also impairs a youth’s competence to make good legal decisions and participate effectively in legal proceedings. Mr. Syed needed some serious adult guidance on how to deal with the fallout of his situation.

But there is little that is systematic in our plea-bargaining processes despite the fact that they fuel our criminal justice system. Plea bargaining is usually informal and unrecorded — sometimes simply fleeting conversations in courtroom corridors. In many jurisdictions, judges are expressly prohibited from participating in it. Attorneys for defendants plea-bargain most cases early and aggressively. But not always, and financial incentives for lawyers may lead them to do otherwise. A study conducted by the behavioral scientist James Anderson and the economist Paul Heaton in The Yale Law Journal revealed disturbing disparities in the outcomes of murder cases in Philadelphia: Public defenders achieved significantly better outcomes with fewer trials than their private court-appointed counterparts, who were paid more if the case went to trial.

A New York federal judge, Jed Rakoff, has proposed one reform: plea-bargaining conferences. In sealed proceedings, judges would examine each party’s position and recommend a nonbinding plea bargain. The plan needs to be refined so it allows a defendant to opt out if he publicly acknowledges he understands what he is giving up. The proposal, however, provides a layer of review to protect the innocent from being pressured into pleading guilty, while potentially encouraging fairer plea bargains through the oversight of a neutral party. It creates a record of plea-bargaining efforts, so there can be no uncertainty as to whether an offer was requested or ignored. Finally, it might help guilty people make a more informed choice about how to resolve their cases.