More than a half-dozen members of the MS-13 street gang “whose primary mission is murder” were indicted Thursday in the brutal killings of two teenage Brentwood girls and a fellow gang member — part of a wave of violence that has terrorized the community, officials said.

The Brentwood teens, Kayla Cuevas, 16, and Nisa Mickens, 15, were killed in September by a group of gang members “swinging baseball bats and machetes.” Eastern District United States Attorney Robert Capers said Mickens was beaten so badly that her face was “almost unrecognizable.”

“For far too long on Long Island, members of the MS-13 have been meting out their own death penalty,” Capers said at a news conference early Thursday afternoon at the federal courthouse in Central Islip.

Capers said the slayings “exemplify the depravity of a gang whose primary mission is murder.”

In the months before those slayings, Cuevas “was involved in a series of disputes with members and associates of the MS-13, including disputes over social media,” federal prosecutors John Durham, Raymond Tierney and Paul Scotti said in court papers.

The prosecutors said four of those indicted as well as two juveniles charged in the case had gone “hunting for rival gang members to kill.” They inadvertently came across Cuevas, and her friend Mickens, and killed them, prosecutors said.

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“Kayla Cuevas, she ran for her life. She was beaten about her face and body with baseball bats and machetes,” Capers said.

The prosecutors said that the MS-13 member, Jose Pena-Hernandez, 18, was killed because he was suspected of “violating the gang rules in several ways, including talking to law enforcement.” Pena-Hernandez was also marked because he was believed to be gay, sources said.

From left, Brentwood High School juniors Nisa Mickens,15, and Kayla Cuevas, 16, were killed in what a police official called a "brutal attack." They were found dead, less than 24 hours apart, in mid-September 2016. Read more
Photo Credit: Family / SCPD

The skeletal remains of Pena-Hernandez, found on the grounds of the Pilgrim Psychiatric Center, “bore the marks of repeated stab wounds,” Capers said.

“Whether you live in Brentwood or the Hamptons, you have a right to safety and security in your neighborhood,” FBI Assistant Director-in-Charge William F. Sweeney Jr. said. “That’s why we’re here today, and it’s the reason we’re not going away.”

Suffolk County Police Commissioner Timothy Sini said that the day the girls “were heinously murdered,” the department “made a commitment to their families and to the residents of Brentwood that justice would be served.”

The 41-count indictment was the culmination of a multi-jurisdictional effort targeting a violent gang that “continues its efforts to expand and entrench itself in our communities, both by sending gang members to illegally enter the United States from Central America, and by recruiting new members from our schools and neighborhoods,” Capers said.

Involved in the six-month investigation were federal prosecutors, the FBI’s Long Island gang task force and Suffolk and Nassau police.

Two other juvenile gang members, not publicly identified, were also charged in the September killings of the two teenage girls and one other juvenile was charged in the October killing of Pena-Hernandez, sources said. Juveniles are not usually publicly identified in federal court proceedings.

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While federal law allows the prosecution of youths under 18 as adults for violent crimes, it would take a judge’s ruling to permit such action.

Two other adult members of MS-13 who were charged were already in custody and two others charged are being sought in the killing of Pena-Hernandez, officials said.

The new charges were added to an indictment last year charging five members of the gang with four other murders between 2013 and 2015, officials said. As many as three to six other recent unsolved killings and disappearances of people in the area may also involve MS-13, sources say.

Investigators believe the recent violence is related to the arrival in the Brentwood area of about a dozen members of MS-13 from Central America in their teens or early 20s, the sources said.

The relative newcomers are steeped in the extreme violence of gang culture in countries such as El Salvador and they have found a niche because federal prosecutions have taken a number of longtime MS-13 members off the streets, the sources said.

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Ten were residents who came in to the country illegally, two were United States citizens and one was a green card holder, Capers said. The cases were combined in one superseding indictment.

Charged publicly yesterday in the killings of Cuevas and Mickens were: Alexi Saenz, 22, of Central Islip, the leader of an MS-13 chapter or clique; his brother, Jairo Saenz, 19, of Central Islip, the no. 2 in the clique; Enrique Portillo, 19, of Brentwood; and Selvin Chavez, 19, also of Brentwood.

They pleaded not guilty at arraignment before U.S. District Judge Joseph Bianco in federal court in Central Islip and were held without bail as a danger to the community and a risk of flight.

Their attorneys declined to comment afterward, as did Durham, Tierney and Scotti.

Because the four are eligible for life in prison or the death penalty, the judge said he would also appoint for each a second counsel who specializes in death-penalty cases, as is typical in such proceedings.

The two people charged publicly in the killing of Pena-Hernandez, German Cruz,18, of Brentwood, and Elmer Alexander Lopez, 19, of Central Islip, are scheduled to be arraigned on the indictment at a later date, according to officials.

Mickens’ father, Robert, 39, learned about the arrests shortly before 9:30 a.m. when a Newsday reporter called him for comment.

“Wow!” Mickens said. “I hadn’t heard anything. I’m shocked because usually cases like this take a long time, and this is moving pretty fast.” Mickens said the arrests will bring some relief to himself and his wife, Elizabeth Alvarado, and Nisa’s siblings, brother Andres, 22, and sister Eliza, 25.

“It’s justice,” Mickens added. “That’s all we want is justice, and for this gang violence to end in America and across the world.”

Federal agents and Suffolk police began an intensified crackdown on gang members in the Brentwood area after the September killings.

Police officials said that since the killings of the two girls, 125 MS-13 members have been charged with state crimes, including drug and gun possession, and seven have been handed over to federal officials for federal prosecutions.

After the Cuevas and Mickens killings, investigators found the skeletal remains of three teenage boys, in or near the Pilgrim Psychiatric Center grounds, two of whom had been reported missing several months before — and all possibly linked to further MS-13 killings.

In addition to Pena-Hernandez, those reported missing were Oscar Acosta, 19, of Brentwood, a student at the Ross Center, whose remains were found on Sept. 16; and Miguel Garcia Moran, 15, of Brentwood, a student at Brentwood High’s Sonderling Center, whose remains were found on Sept. 21.

Also in October, Dewann A.S. Stacks, 34, of Brentwood, was found beaten to death on American Boulevard, in what police said was a gang-related killing.

The gang-related violence continued this year, police said, when Esteban Alvarado-Bonilla, 29, of Brentwood, was shot to death on Jan. 30 in a Central Islip deli on the Brentwood border.

Since 2002, federal prosecutors working with the FBI task force and local police have convicted several hundred MS-13 members, officials have said. The MS-13 membership, however, is often refilled in several years by “the brothers” of those convicted, referring to younger gang members from Central America, sources have said.

— With Lisa Irizarry