Marbury versus Madison was part of a Federalist part to preserve influence with the Federal Government once the Federalists were voted out of office in 1800. In the last days of the Adams Administration a whole series of Federal officers were appointed by Adams and approved by Congress. Some of those people did not arrive in the capital in time to take their appointments before the new administration took office. The New President refused to accept these appointments. One of the appointees sued. In Marbury versus Madison, John Marshal affirmed the right of Jefferson to refuse their appointment but established a ruling which ruled:
“All laws which are repugnant to the Constitution are null and void.” Marbury vs Madison 5 U.S. 137, 174, 176.
“The general rule is that an unconstitutional statute, though having the form and name of law, is in reality no law, but is wholly void and ineffective for any purpose; since its unconstitutionality dates from the time of its enactment… In legal contemplation, it is as inoperative as if it had never been passed… Since an unconstitutional law is void, the general principles follow that it imposes no duties, confers no rights, creates no office, bestows no power or authority on anyone, affords no protection and justifies no acts performed under it… A void act cannot be legally consistent with a valid law. Indeed, insofar as a statute runs counter to the fundamental law of the land, it is superceded thereby. No one is bound to obey an unconstitutional law and no courts are bound to enforce it.” 16 Am Jur 2d S177, late Am Jur 2d S256”
This angered Jefferson, and over time it angered him more. He saw this decision as the “usurp[ation] of exclusively explaining the constitution.” And over time he realized that:
“the constitution had deprived the people control “Over the judiciary department.” And that therefore he wrote that even after years of Republican government the Federalists “ therefore, has continued the reprobated system, and although new matter has been occasionally incorporated into the old, yet the leaven of the old mass seems to assimilate to itself the new, and after twenty years' confirmation of the federal system by the voice of the nation, declared through the medium of elections, we find the judiciary on every occasion, still driving us into consolidation.” 
The Republicans could not do things in the national interest, or enforce their conception of what is constitutional or not because the Supreme court was dominated by Federalists appointed by Adams and would strike down their laws as unconstitutional. In Jefferson’s view:
“The constitution, on this hypothesis, is a mere thing of wax in the hands of the judiciary, which they may twist, and shape into any form they please”
Jefferson felt that the constitution had made the Supreme Court a potential locus of absolutist and undemocratic government:
“It should be remembered, as an axiom of eternal truth in politics, that whatever power in any government is independent, is absolute also; in theory only, at first, while the spirit of the people is up, but in practice, as fast as that relaxes. Independence can be trusted nowhere but with the people in mass. They are inherently independent of all but moral law.”
Jefferson believed that:
“each department [should be] truly independent of the others, and ha[ve] an equal right to decide for itself what is the meaning of the constitution in the cases submitted to its action; and especially, where it is to act ultimately and without appeal.”
Jefferson was referring to the autonomous right of each branch of government (Judiciary, executive, and legislative”) to decide its own cases. In some cases the judiciary has since respected Jefferson’s perspective but not in all. They typically defer to the executive on some legal matters. So, while the Judiciary has frequently overruled the executive and the legislative on matters where the court assumes the executive knows what they are doing [which is what Jefferson is inferring]. This is sometimes appropriate. Thus the courts have protected the rights of minorities and the oppressed, but sometimes the appeal to the Supreme Court has been an instrument of tyranny [Private Separate Advantage].
A “mere thing of wax in the hands” of either Judges or Executive.
To me Marbury Versus Madison exposed a process issue where both sides had issues that needed to be resolved, not with merely the courts overriding the executive, but with better process. Andrew Jackson applied Jefferson’s theory when the Supreme Court overruled his decisions on ethnic cleansing of American Indian Indigenous peoples living in territories he had control over. He told the court ‘you made the decision, now you enforce it” and then dispossessed and murdered thousands of human beings with impunity. The executive with the concurrence of docile courts or in spite of them have also treated the constitution as a “thing of wax.”
When there is injustice there needs to be judicial review. But that review in many cases deserves to be heard by an independent jury, prosecuted by experts representing all legitimate points of view, and subject to the old principle of separation of powers; “No man should be judge, jury and executioner, in the same case. Jefferson rightly noted:
“The nation declared its will by dismissing functionaries of one principle, and electing those of another, in the two branches, executive and legislative, submitted to their election. Over the judiciary department, the constitution had deprived them of their control.”
On first perusal, it is hard to see how the nation could establish democratic controls over the Judiciary. But there is an age old way, which while under assault in our modern times, represents an even more pure exercise of democracy than that of elections. It is the Jury. A body of independent citizens, not ignorant or totally unbiased, but selected at random from the general population, could form commission style juries that could make better, more fair, and more representative decisions than a panel of paid permanent jurists who are selected from professional judges and serve for life. The ancient Greeks didn’t trust to elections, they believed that volunteers should directly make decisions, and in our modern society volunteers, national guard, and juries are the best democratic institutions we still have. The process problem Jefferson identified with Marbury versus Madison is in how to have judicial controls on decision making that represent the people, and not special interests such as the Federalists represented in his times.
If disputes were subject to jury review [Juridical Controls, Judicial Oversight] in the governments departments and agencies, there too would be better process. For independent juries composed of a representative (and temporary) sample of the American people would embody Jefferson’s principle that ”Independence can be trusted nowhere but with the people in mass.” The purest expression of democracy in action is the Jury. If a jury had ruled on Marbury versus Madison, what would Jefferson have been willing to say?
 Reference is to John locke’s definition of tyranny in “Twin Treatises on Government”