Thomas Modly resigns following criticism of his handling of a crisis involving the USS Theodore Roosevelt.
"He resigned on his own accord, putting the Navy and the sailors above self so that the USS Theodore Roosevelt, and the Navy, as an institution, can move forward," Mr Esper said in a statement.
In addition to the health threat posed to the crew of more than 4,800 sailors, the outbreak has sidelined the warship indefinitely and created conflict at the highest levels of the Pentagon. Mr Esper had publicly expressed his support for Mr Modly's decision to fire Captain Crozier, but after Mr Modly's speech about the ship, Mr Esper grew unsettled.
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