Brief Summary
The Set-Up
The Imperial Japanese Navy Air Service bombs the U.S. military base at Pearl Harbor, Hawaii Territory, drawing America into World War II. Back on the mainland, xenophobic war hysteria and anti-Japanese racism spread like a California wildfire.
The Text
E.O. 9066 issues special permissions for the secretary of war and his associates to create military zones that they fully control—all in consideration of national defense.
Now, that's a lot of power.
Some of that power includes being able to determine who occupies those zones and who doesn't. This means that certain people who are considered "dangerous" to the peace and security of the nation can be forcibly expelled from the military areas. Most of the people expelled were Japanese Americans.
If such drastic measures seem unfair, it's because they are. Super unfair. But FDR is careful to cite legal and historical precedents to justify and uphold his declaration.
TL;DR
E.O. 9066 gives the secretary of war power to create special military exclusion areas and unjustly sweep away suspicious citizens (i.e., 120,000 Japanese Americans) from the West Coast and dump them in inland internment camps.
History would remember this as the U.S. government acting very much in the wrong.