Washington CNN  — 

Secretary of Defense James Mattis and the State Department’s anti-ISIS envoy, Brett McGurk, bid farewell to their respective departments Monday after parting ways with President Donald Trump’s administration over his plans to reduce the American presence in Syria.
Mattis told Pentagon employees to “keep the faith in our country” and McGurk wished his former colleagues well “as they work under extremely difficult circumstances to protect the interests of our great country.

“Our Department is proven to be at its best when the times are most difficult,” Mattis wrote in a message to Defense Department employees. “So keep the faith in our country and hold fast, alongside our allies, aligned against our foes.”

Mattis also expressed confidence in the department’s leadership as his deputy defense secretary, Patrick Shanahan, prepares to take over as acting secretary.

“Our Department’s leadership, civilian and military, remains in the best possible hands. I am confident that each of you remains undistracted from our sworn mission to support and defend the Constitution while protecting our way of life,” his statement read.

Mattis concluded, “It has been my high honor to serve at your side. May God hold you safe in the air, on land, and at sea.”

In a tweet, McGurk, who worked in the State Department, said that he wishes his “former civilian and military colleagues well as they work under extremely difficult circumstances to protect the interests of our great country. It was a privilege to serve alongside them.”

The former four-star Marine Corps general, whose last day is Monday, announced his resignation in late December with a letter saying his views were not aligned with those of President Donald Trump, who had just announced plans to withdraw US troops from Syria.

“Because you have the right to have a Secretary of Defense whose views are better aligned with yours on these and other subjects, I believe it is right for me to step down from my position,” Mattis wrote in his letter to the President.

McGurk, whose last day was Monday, submitted his resignation a day after Mattis. Two senior officials and several sources familiar with his thinking told CNN he did so in response to Trump’s decision to withdraw US troops from Syria.

On Monday, the Pentagon will hold a government-wide call between Mattis and Shanahan to mark the transition of power at the Defense Department.

A defense official said the call is meant “to ensure all members within the government know who is in command” and is “a courtesy and a mark of respect for the incoming Secretary of Defense.”

A former corporate executive, Shanahan’s portfolio at the Department of Defense has been narrow, with no experience in international affairs or counterterrorism. As Mattis’ No. 2 in the Pentagon, Shanahan almost exclusively handled internal reform, budget issues and the Space Force, the new military branch proposed by Trump.

CNN’s Barbara Starr contributed to this report.