President Trump issued an order late Friday that supports a ban on many transgender troops, deferring to a new Pentagon plan that essentially cancels a policy adopted by the Obama administration.

The decision revokes a full ban that Trump issued last summer but disqualifies U.S. troops who have had gender reassignment surgery, as recommended by Defense Secretary Jim Mattis.

“By its very nature, military service requires sacrifice,” Mattis wrote in a memo to the president that was released Friday. “The men and women who serve voluntarily accept limitations on their personal liberties — freedom of speech, political activity, freedom of movement — in order to provide the military lethality and readiness necessary to ensure American citizens enjoy their personal freedoms to the fullest extent.”

Current transgender service members who have not undergone reassignment surgery should be allowed to stay, as long as they have been medically stable for 36 consecutive months in their biological sex before joining the military and are able to deploy across the world, Mattis recommended.

Mattis recommended that anyone diagnosed with gender dysphoria, the condition of wanting to transition gender, since the Obama administration ended the Pentagon’s longtime ban on transgender service in 2016 may continue to serve. The decision amounts to a “grandfathering” of those affected by the new policy.

The new plan will be challenged in court, just as the full ban that Trump issued last summer was, in at least four separate cases that are still ongoing. Federal judges allowed transgender service members to continue serving under the old ban and permitted transgender recruits to join the military as well.

The Justice Department filed a copy of Mattis’s recommendations in at least one of those legal battles Friday.

“In service to the ideological goals of the Trump-Pence base, the Pentagon has distorted the science on transgender health to prop up irrational and legally untenable discrimination that will erode military readiness,” said Aaron Belkin, who has studied transgender issues for the Palm Center, a think tank that had worked with the Obama administration in repealing the previous ban. “There is no evidence to support a policy that bars from military service patriotic Americans who are medically fit and able to deploy. Our troops and our nation deserve better.”

In his memo to the president, Mattis specifically challenged the thinking of the Obama administration when it repealed the ban in 2016. Mattis said that he found a Rand Corp. study — commissioned by the Pentagon under Obama that became a backbone of the repeal process — to be flawed.

“It referred to limited and heavily caveated data to support its conclusions, glossed over the impacts of health care costs, readiness and unit cohesion, and erroneously relied on the selective experiences of foreign militaries with different operational requirements than our own,” Mattis wrote. “In short, this policy issue has proven more complex than the prior administration or RAND assumed.”

The new direction comes after months of the Pentagon’s grappling with how to change its policy after Trump unexpectedly tweeted July 26 that he was banning all transgender people from serving in the military. The president, without any plan in place, cited the “tremendous medical costs and disruption” that he believed transgender military service would cause, and said that he had consulted with “my Generals and military experts.”

A day later, Marine Gen. Joseph F. Dunford Jr., the chairman of the Joint Chiefs of Staff, released a memo effectively stopping the military from making any changes until a new policy was adopted, and Mattis backed the move.

In August, Trump issued a presidential memorandum providing more detail. He accused the Obama administration of allowing transgender military service without identifying a “sufficient basis” that doing so would not “hinder military effectiveness and lethality, disrupt unit cohesion, or tax military resources,” and he directed Mattis to have the Pentagon adopt a new ban similar to the military’s former policy by Friday.

The Obama administration began allowing transgender people to serve openly in the military in June 2016, following a review that dragged out months longer than expected amid internal conflict in the Pentagon over how the change would be made. Until then, the Pentagon considered gender dysphoria a disqualifying mental illness.

In removing the ban, then-Defense Secretary Ashton B. Carter stopped the military from involuntarily separating anyone in the service, and gave the service branches a year to iron out how they would begin processing transgender recruits. A year later, Mattis delayed allowing transgender recruits for an additional six months as the deadline neared, saying the issue needed more study.

Trump’s tweets came a few weeks later.

Federal judges required the military to allow transgender recruits beginning Jan. 1, and the Pentagon signaled in December that it would not stand in the way of the courts’ rulings. Instead, it issued new policy guidance to recruits to explain how to enlist transgender men and women, and stated in a policy paper that the guidance “shall remain in effect until expressly revoked.”