One expected witness is Humberto Navarrete, whose grainy cellphone video at the San Ysidro port of entry captured audio of a man believed to be Hernandez pleading for help and passers-by asking that he be left alone, one person said. The other was a companion of Navarrete that night.
Mitchell Rivard, a Justice Department spokesman, said the case remains under investigation and declined further comment.
Hernandez, 42, was shot by agents in May 2010 at the busy border crossing as he was being returned to Tijuana, Mexico. Mexican President Felipe Calderon joined a chorus of critics who complained of excessive force by U.S. Customs and Border Protection officials, none of whom have been publicly identified.
An autopsy by the San Diego County coroner's office found Hernandez died of a heart attack, with a heart condition and methamphetamine use listed as contributing factors. The autopsy said Hernandez was unresponsive shortly after he was shot with a stun gun, apparently three or four times.
The coroner's report, citing a San Diego police detective, said Hernandez was "agitated and confrontational" after he was detained by Border Patrol agents crossing the border illegally and became "suddenly violent" when his handcuffs were removed at the border crossing.
It is unclear if the evidence being presented to the grand jury will lead to criminal charges or who is the target of the investigation. Still, the convening of a grand jury suggests the government is interested in bringing charges.
"When a prosecutor looks at a case, you can decide no crime has been committed, you close the case and move on. That obviously hasn't happened in this case," said Peter Nunez, a former U.S. attorney in San Diego who is not involved in the case. "The fact that there's a grand jury means it has progressed to the next level, if you will."
Nunez cautioned that prosecutors may have determined there wasn't enough evidence to justify charges but sought political cover with a grand jury.
"This case has so much publicity attached to it," he said. "You can see a prosecutor saying, 'There's not enough evidence to justify criminal charges ... I'm going to present the case to the grand jury, with the idea that the grand jury may decide not to indict.' The prosecutors are shielded from criticism to some degree."
The decision to present evidence to a grand jury and potentially charge Customs and Border Protection officials comes at a time when the Justice Department and Attorney General Eric Holder are under intense criticism from Republicans for a botched gun-tracking operation known as Fast and Furious. In that operation, agents of the federal Bureau of Alcohol, Tobacco, Firearms and Explosives in Arizona abandoned the usual practice of intercepting all weapons they believed to be illicitly purchased.
The agents in Fast and Furious lost track of several hundred weapons. In 2010, Border Patrol Agent Brian Terry was killed in a firefight with a group of armed Mexican bandits and two guns traced to the operation were found at the scene.
Navarrete released his cell phone audio to reporters immediately after Hernandez died.
The investigation attracted renewed scrutiny and criticism less than three months ago after another eyewitness video that aired on PBS appeared to show Hernandez being shot while lying on the ground, surrounded by about a dozen agents. Sixteen members of Congress wrote Homeland Security Secretary Janet Napolitano to say Hernandez's death "may be emblematic of broader structural problems."
It is extremely rare for U.S. border authorities to face criminal charges for deaths or injuries to migrants. In April, federal prosecutors said there was insufficient evidence to pursue charges against a Border Patrol agent in the 2010 shooting death of a 15-year-old Mexican in Texas.