Well, part of the genius of John Marshall was his selection of the
Marybury case to claim the Court's power to declare a law unconstitutional. Because the court decided against Marbury and in favor of the Jefferson administration, there was nothing for anyone to do following the case. Jefferson could not refuse to abide by the ruling because the decision was technically in his favor (the Court decided that Jefferson's Secretary of State did not have to deliver to Marbury a commission making him a justice of the peace).
So, all President Jefferson could do was sit and watch. And seethe. He really disliked Chief Justice Marshall.