Kony is wanted by the International Criminal Court for war crimes and he and his militia have been accused of killing thousands of civilians and abducting thousands of children during his decades-long insurgency in Uganda and neighboring countries.
The US began the transition last week, a US defense official told CNN, and it's due to be completed by September. A team of elite US troops recently pulled out of Camp Dungu, a remote outpost in the Northwestern part of the Democratic Republic of the Congo that was also once an area of operations for Kony's insurgency.
According to Africa Command, which oversees American military operations on the continent, the US forces involved in the counter operation against the Lord's Resistance Army will now "transition to broader-scope security and stability activities that continue the success of our African partners."
Reasons for withdrawal
US officials have cited a diminished LRA and other priorities as the reason for the decision to withdraw.
"The extent of LRA attacks and related deaths has dropped significantly over recent years, and the number of LRA fighters has decreased dramatically," Robyn Mack, a spokeswoman for Africa Command, told CNN in an email.
A statement from US Africa Command said that African forces involved in the hunt helped reduce the number of LRA fighters from "nearly 2,000" to "under 100" and captured four of the LRA's five top leaders.
"The bottom line is, this operation, although not achieving the ability to get to Kony himself, has essentially taken that group off the battlefield and for the last several years, they've really been reduced to irrelevance," Gen. Thomas Waldhauser, the commander of Africa Command, told reporters at the Pentagon in March.
Threat remains with Kony free, groups say
Outside groups, however, have warned that with Kony free, the risk to the region remains
"The LRA will pose a serious risk to civilians as long as Kony is allowed to roam freely across central Africa," said Paul Ronan, director of research and policy at Invisible Children
, a nonprofit group that advocates for children and communities affected by the long-running conflict.
Ronan acknowledged the mission's impact, saying it significantly helped reduce the number of civilians killed by Kony's forces.
But he called the planned ongoing withdrawal "disappointing," adding that "the decision by the US and Ugandan troops to withdraw before the job is finished leaves the LRA with an opening to ramp up recruitment of child soldiers and resume large-scale massacres."
"The US should continue supporting efforts to apprehend Kony and encourage defections (of his fighters)," Holly Dranginis, a senior policy analyst for the Enough Project
, told CNN.
Dranginis, whose analysis focuses on the Lord's Resistance Army and the surrounding region, added that "Kony's power is much diminished since his heyday years ago but bringing him to justice remains a worthwhile goal for intelligence-gathering and fulfilling the rights of victims."
Even if the US troops were to stay, though, their effectiveness would be in doubt as the main provider of troops to the mission -- Uganda -- similarly announced its intent to withdraw
from the hunt in April, also citing the mission's success at eliminating insurgents.
"The decision to withdraw was premised on the realization that the mission to neutralize the LRA has now been successfully achieved," Brig. Gen. Richard Karmemire, a spokesman for the Ugandan Ministry of Defense, said in a statement issued last month. "(Kony) no longer poses any significant threat to Uganda's security."
Origins of a terror group
While originally founded in Uganda, the LRA operates in small groups in the border regions of the Democratic Republic of Congo, the Central African Republic, South Sudan and Sudan. The group sought the overthrow of the Ugandan government while also adhering to an extreme fundamentalist religious view.
Kony and the LRA have been active in Uganda and neighboring countries since the 1980s and Kony has been accused of killing thousands of civilians and abducting children to serve as soldiers in his militia.
The International Criminal Court issued a warrant for Kony's arrest in 2005, accusing his organization of carrying out war crimes and crimes against humanity, including murders, abductions, sexual enslavement, mutilations and lootings.
The US State Department has offered up to $5 million for information leading to his arrest, transfer or conviction.
"KONY 2012," a documentary film on Kony's crimes, received millions of views on Youtube, helping to raise awareness of Kony's activities internationally and prompting calls for his capture.
A UNICEF study estimated that at least 66,000 children and young people were abducted by the Lord's Resistance Army between 1986 and 2005. Nearly 2 million people were displaced by the violence during the conflict.
"He is one of the most brutal and deplorable warlords in the region," Jennifer Cooke, director of the Africa Program at the Washington-based Center for Strategic and International Studies, told CNN.
Cooke added that while Kony "poses very little direct threat to US interests," the US role in the mission was brought about due to pressure from the American public and a few members of Congress.
But the public and Congress' focus has shifted with the rise of the war crimes committed by newer terror groups like ISIS.
US troops saw some instances of combat in operation
While American forces have largely been in a supporting role, primarily providing support to an Africa Union-led task force with troops from Uganda, South Sudan, the Democratic Republic of the Congo and the Central African Republic, there have been occasions where US troops have found themselves in combat.
Two US military officials told CNN that a US service member participating in the multinational operation shot and killed an LRA member last month during a mission in the Central African Republic.
The US service member was escorting a peacekeeper from the CAR-based African Union force when they came upon two LRA fighters. The officials said that one of the LRA soldiers attempted to draw his weapon, prompting the US Special Operations member to shoot him.
Does decision equal shift in policy?
The US withdrawal has also left some observers wondering whether the change might signal a shift away from purely humanitarian missions that don't have an immediately discernable direct impact on American security.
Since the US role in the hunt for Kony began, Africa has seen the rise of insurgencies with links to global terror groups seen as plotting to directly attack the US and its allies, including Boko Haram in Nigeria, ISIS in Libya, and al Qaeda in the Maghreb in northwest Africa and Al-Shabaab in Somalia.
The US and Africa Command are involved in helping local allies battle these groups across Africa.
Could LRA rebuild?
Cooke warned that there was a chance that the end of the hunt could enable Kony and his allies to reconstitute their scattered forces, taking advantage of their involvement in wildlife trafficking, poaching, criminal activity and looting.
"They could regrow," she said.
It was a sentiment echoed by Waldhauser during a conference call with reporters.
"We obviously have some concerns about the possibility of the LRA coming back to fruition, (or) there could be another group in that area that would come up and fill that void," he said.
"We are certainly aware of the fact that we don't want to leave a void there," he added. "We'll keep a close eye on it, but the time has come to move forward because the organization itself is really in a survival mode and has very little, if any, relevancy."