(CNN) -- A Mexican man was arraigned in a federal court Friday for the murder last December of a U.S. Border Patrol agent in Arizona, as well as 13 other charges.
U.S. District Court Magistrate Jacqueline Marshall unsealed the indictment against Manuel Osorio-Arellanes at Arellanes' arraignment in Tuscon, Arizona. Besides second-degree murder, charges against Arellanes include three counts of assault of a federal officer and four counts of using a firearm to commit a violent crime, three counts of re-entry of a deported alien and two counts of illegally possessing a firearm.
In a press release, the office of U.S. Attorney Dennis Burke of Arizona noted that similar charges will be forthcoming against Arellanes' co-defendants -- who are fugitives -- though their identities remain under seal.
"Today's indictment is an important step in the case, but it is only a first step to service justice," said Burke. "This is an active ongoing investigation that is making more and more progress every day."
In an FBI affidavit, Special Agent Scott Hunter said the Border Patrol agents, using thermal binoculars, spotted a group of "at least" five people believed to be illegal aliens around midnight in Peck Canyon near Rio Rico, Arizona, not far north of the border town of Nogales.
As the group drew near, one of the agents identified himself as an officer and ordered the men to drop their weapons.
"When the suspected aliens did not drop their weapons, two Border Patrol Agents deployed 'less than lethal' bean bags at the suspected aliens," Hunter wrote. "At this time, at least one of the suspected aliens fired at the Border Patrol Agents," striking Terry, Hunter wrote.
Then two agents returned fire with a long gun and a pistol, striking one of the men in the group, Hunter wrote.
The group the agents encountered were armed "border bandits," according to T.J. Bonner, head of the agents' union. He said these people typically try to accost illegal immigrants and steal whatever money or possessions they have.
Terry was shot in the exchange and later died, Johnson said.
Arellanes was apprehended after being wounded in the firefight. Since being treated medically, he's been in federal custody on felony immigration charges. The U.S. Attorney said Friday that his co-conspirators -- including the person suspected of firing the shot that led to Terry's death -- fled and remain at large.
A spokesman for that office, Robbie Sherwood, explained that all members of the bandit group can be held responsible and be charged with murder under U.S. law, not just the shooter. Three men were apprehended soon after, and not far from, the shooting site but last month authorities announced they had no connection with Terry's death, Sherwood noted.
The indictment released Friday contends that Arellanes and his "co-conspirators" killed Terry "with malice," having earlier come together and agreed to "assault" him and three other Border Patrol agents.
At least two of the suspects -- one of them being Arellanes, who is from El Fuerte, Mexico -- carried assault rifles at the "ready" position, equipped with 25 rounds of ammunition, while patrolling the area in single-file formation, the court document said.
Arellanes, also referred to as "Paye," had re-entered Arizona despite being deported from the United States three times last year -- in February, June and October -- according to the indictment.
His trial is scheduled to begin June 17 in Tucson, to be presided over by U.S. District Court Judge David Bury, according to the U.S. Attorney's office.
In a statement released Friday evening, Homeland Security Secretary Janet Napolitano applauded the indictment "as an important step in seeing that justice is served for this unconscionable crime" and indication of America's intent to protect its Border Patrol agents.
"We will not stand for aggression against our men and women in uniform, and we will bring the full resources of the federal government to bear in protecting them from harm and holding accountable those who would threaten their lives or their safety," she said.
The incident set off a flurry of questions over whether or not the border patrol officers were armed with only the non-lethal "bean bag" guns described in the FBI affidavit.
Napolitano wrote last month to Sen. Charles Grassley, R-Iowa, that the officers were empowered to defend themselves and were equipped with a combination of lethal and non-lethal weapons.
That included Terry, who carried a HK P2000 handgun and an M4 long rifle on the night of his death, Napolitano said.
CNN's Greg Botelho contributed to this report.