When Jason Jones was arrested in a fatal shooting in the Bronx in May, he told the police that he had been nowhere near the scene. He said he had left work, ridden the bus with some co-workers and cashed his paycheck, and later had taken a subway to see his girlfriend.

Federal prosecutors charged Mr. Jones and his older brother, Corey, in the shooting, saying they had killed the victim because he had been a government witness in drug and gun cases. Both men could face the death penalty if the government decides to seek it.

But in recent weeks, the case has taken an extraordinary turn  because of Jason Jones’s MetroCard.

Months after the arrests, a retired detective working for Mr. Jones’s lawyers drove to a city jail located on a barge moored in the East River in the South Bronx, where Mr. Jones had been held after his arrest, and retrieved his wallet. The MetroCard was still inside.

Mr. Jones’s lawyers then asked New York City Transit to use the card to trace his movements the night of the shooting. The results supported his account, showing that the card had been used on a bus, and later on a subway roughly five miles from the shooting, just as he had described.