When are governments allowed to override our individual liberties?

In a western democracy like the United States for example, citizens have many rights that keep state and the national government out of one's affairs. There is also a large number of civil rights that the US Constitution protects and rightly so. In cases of a national emergency, however, the Constitution allows the US president, for example to suspend a good deal of individual rights. With that said, a president can for example the writ of habeas corpus. Any time such rights are suspended, however, the US Supreme Court will review the validity of any civil rights suspensions by either the Congress or the executive branch.