What is one way that the Judicial Branch can overrule the Executive Branch?
By Constitutional standards, the Executive Office was never intended to have a legion of alphabet soup agencies under it as it now has. The creation of law was to be the domain of Congress, or the Legislative Branch, rather than governance by "executive orders," which cannot be repealed, and about which the Constitution says nothing. These have the force of law, but are not laws, merely "policies." Currently the Judiciary acts (or used to act) as a check on such executive orders and could nullify them. It appears that the original check of the Executive by the Judiciary was, as has been previously stated, that the Rule of Law was supreme, and no one, not even the President, was above it and could not escape consequences to actions; rather, the president was subject to the same laws as any citizen, and moreover, could be impeached and removed from office for "high crimes and misdemeanors." Presumably, the Judiciary would uphold a conviction of such a crime if the President were proven guilty.
With its power of Constitutionality, the judicial branch is able to limit the power of the executive branch. The judicial branch is able to interpret the Constitutionality of the actions of the executive branch. If it decides to act in a manner that is against or contrary to the spirit of the Constitution, it has the ability to declare these actions "Unconstitutional" and strike down the action. This is important for a variety of reasons. The first is that the judicial branch's ability to determine Constitutionality allows it to act as the protectorate of the Constitution, under which all branches, including the executive, must be responsible. Another reason why this is important is because underscores the assumption in the Constitution that no one, not even the President, is above the law.
The most important way that the judicial branch can have a check on the executive branch is by overturning executive orders issued by the executive.
The executive branch, headed by the president, can make policy to some extent by issuing executive orders. These tell government agencies to do various things. They can be issued without having to go through Congress.
But these orders, like actual laws, can be challenged in court. The judicial branch can rule that the orders violate laws passed by Congress and it can rule that they violate the Constitution. In either case, the orders would be ruled illegal.
The Judicial Branch has a check on the Executive Branch by the simple fact that the justices appointed to the Supreme Court, once nominated by the President and approved by the Senate, have no end to their term of office. They can stay until they retire or die if they want. This makes them independent of the rest of government, the Executive Branch included. So if they were to rule on a case in a way the President didn't like, there would be nothing the President could do about it.