Cecily Aguilar, 22, has been charged with one count of conspiracy to tamper with evidence.
The Army said Aguilar is the estranged wife of a former soldier who was stationed at Fort Hood.
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Aaron David Robinson, a 20-year-old Army Specialist, was identified as the person of interest in Guillen's case. She disappeared in April. Robinson died by suicide when authorities made contact with him on Wednesday, according to special agent Damon Phelps with the Army's Criminal Investigation Command.
Robinson allegedly admitted to Aguilar that he transferred the woman's body off the base to a remote site in Bell County.
"Subsequently, Robinson enlisted the help of Aguilar in disposing of the dead female's body," read a news release issued Department of Justice U.S. Attorney's Office - Western District of Texas.
According to the criminal complaint, on June 21, what appeared to be the burned remains of a plastic tote or tough box were found in an area near where Robinson's phone pinged. No remains were found that day.
Around 1 p.m. on June 30, contractors working on a fence near the Leon River discovered what appeared to be human remains. When authorities searched the area, they found scattered human remains that appeared to be placed into a concrete-like substance and buried.
According to investigators, Aguilar admitted that Robinson told her he killed a female soldier by striking her in the head with a hammer multiple times at his arms room while on post on April 22, the same day Guillen went missing.
RELATED: What we know about Fort Hood soldier Vanessa Guillen since her disappearance in April
The criminal complaint said Robinson then placed Guillen's body in a box and moved the box to a location near the Leon River.
Aguilar told officials that sometime between the evening of April 22 and the early morning of April 23, Robinson picked her up at the gas station where she worked and took her to an area near the Leon River and a bridge. A box with wheels and handles was already at the site.
Aguilar said Robinson walked her over to the woods, opened the box, and she saw a dead woman inside. Aguilar later told investigators she "recognized the deceased whom she helped Robinson mutilate and dispose of" as Guillen.
The complaint said Aguilar and Robinson then used a hatchet or ax and a machete-type knife to dismember the body. They allegedly tried to burn the body, and placed the remains in three separate holes and covered them up.
The remains found in a shallow grave near the Leon River in Bell County have yet to be formally identified by authorities.
Aguilar faces up to 20 years in prison and with a maximum $250,000 fine, if convicted.
She's currently being held at the Bell County jail. Her first court appearance will be in Waco.
The hearing is expected to take place early next week.