Ultimately the Commander in Chief is in control of the National Guard.
The National Guard serves a dual role. Most of the time, it’s under the control of individual states, with the state governor acting as commander in chief. However, the president can activate the National Guard and place it under federal control. When this occurs, guard units are used to supplement the regular Army, bolstering its forces with additional combat units.
Much moar here >https://science.howstuffworks.com/national-guard.htm
Simply, Potus can Federalize them as Commander in Chief.