Sgt. Elder Fernandes, 23, was last seen Aug. 17 when his staff sergeant dropped him off at his house.
His body was found hanging from a tree on Aug. 27, about 25 miles from the Army post, the Boston Globe reports.
Authorities said they did not suspect foul play in Fernandes' death, though an autopsy was ordered. Formal identification of the body will be determined by the autopsy, but identification found nearby indicated the body belonged to Fernandes.
Fernandes' family welcomed him home Tuesday evening at Boston Logan Airport. The soldier is originally from Brockton, Massachusetts.
Fernandes was given plane-side honors upon arrival.
You can watch the moment his casket, draped with an American flag, was removed from the airplane in the video above.
Yesterday, a month after U.S. Army Sec. Ryan McCarthy admitted failing fellow missing Fort Hood soldier Vanessa Guillen, a shake-up in leadership at the Texas base was announced.
SEE ALSO: Missing Fort Hood soldier's body found, family says
Maj. Gen. Scott Efflandt, who oversaw Fort Hood at the time of Guillen's disappearance earlier this year, is being replaced, as previously announced, but will no longer ascend to take command of the 1st Armored Division.
Instead, according to a military announcement, Efflandt will remain at Fort Hood in a deputy capacity while his successor, Maj. Gen. John B. Richardson IV takes over beginning Wednesday.
"They need an independent investigation," Isabel Fernandes, the once-missing soldier's aunt, told ABC News. "I don't trust the army investigating themselves."
The move also goes along with a new lead investigator being appointed to look at how Fort Hood brass handled Guillen's sexual harassment allegations, which Army officials at one point disputed.
RELATED: Missing Fort Hood soldier reported abusive sexual contact before disappearance
"Our worst nightmare has happened. One of our own, Sergeant Elder Fernandes has been found dead today," family attorney Natalie Khawam told the Boston Globe. "We are sickened by this tragedy that has happened one too many times. We are heartbroken for Elder Fernandes's family."
Prior to disappearing, Fernandes claimed he was the victim of abuse.
"We can confirm that there is an open investigation of abusive sexual contact involving Sgt. Fernandes," Fort Hood LTC Chris Brautigam said in a statement last week. "The chain of command takes all allegations of sexual harassment and assault seriously."