Army officials say Special Agents from the U.S. Army Criminal Investigation Command, along with the U.S. Marshals, Killeen Police Department, and the Lone Star Fugitive Task Force were trying to find the junior soldier who fled from Fort Hood late Tuesday.
Around 1:29 a.m. Wednesday, officers found him in the 4700 block of East Rancier Avenue. Authorities said that as they tried to make contact with the suspect, he pulled out a gun and shot himself.
He died from the self-inflicted gunshot wound.
His name will not be released pending notification of next of kin.
Officials say the civilian suspect arrested in Guillen's case is the estranged wife of a former Fort Hood soldier. She is currently in custody in the Bell County Jail and will be charged.
The Texas Rangers and several other agencies are still processing the scene at Leon River in Bell County, where partial remains, which Guillen's family believes were hers, were found on Tuesday.
While that is not yet confirmed, Texas EquuSearch founder Tim Miller, who was helping look for Guillen, told ABC13, "The search for Vanessa is now over."
READ MORE: Human remains found during search for missing Fort Hood soldier Vanessa Guillen
Positive identification of the remains is pending.
"We have made significant progress in this tragic situation and are doing everything possible to get to the truth and bring answers to the family of Pfc. Vanessa Guillen," said Chris Grey, the spokesman for Army CID.
Guillen, 20, was last seen on April 22 in the parking lot of her Regimental Engineer Squadron Headquarters, 3rd Cavalry Regiment at Fort Hood.
CID Officials say the criminal investigation is ongoing.
"There is still a lot of investigative work to be done and we ask for the public and media's patience," Grey said. "There are obviously pieces of information and evidence that cannot be shared with the public during an active criminal investigation. Doing so can seriously jeopardize the charging and successful prosecution of individuals. When important investigative information is prematurely released, criminals can and will destroy evidence, conspire to change their stories, build false alibis, etc."
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WATCH: "My sister is NO JOKE. My sister is a HUMAN BEING. And I want justice." Lupe, Vanessa Guillen's sister made a powerful statement in the video below.
Vanessa Guillen's sister talks about disappearance
MIRE: 'Mi hermana no es un chiste' Lupe, la hermana de Vanessa Guillen, hace súplica apasionada
Sister of Vanessa Guillen makes passionate plea in Spanish