Thomas Jefferson and John Marshall had much in common. They were both from Virginia, they both modeled the same shaggy styles of the Virginia gentry, and they both attended the College of William and Mary. Both were appointed Secretary of State and both served as minister to France.
They were even related, distant cousins on the Randolph side.
But by 1801, when they arrived in the new capital of Washington City to assume their new positions as respective heads of the executive and judicial branches of government, they found themselves miles apart politically and philosophically. Marshall was a Federalist. Like many who served in the officer corps of the Continental Army, he emerged from the war a nationalist committed to strengthening the central government. As the new Chief Justice of the Supreme Court, Marshall was intent on expanding the Court's authority and using this authority to enhance the power of the federal government.
Jefferson, as a Republican, was just as anxious to reduce the power of the state and restore the principles of limited government he equated with the ideals of the Revolution. He was especially intent on curbing the judiciary's power, as he feared it might become an antidemocratic bastion of Federalist influence.
There was bound to be a collision between the two. But neither realized that the opportunity would be provided by the very first thing that Jefferson chose to do—or rather, not to do.
When John Adams named Marshall Chief Justice of the Supreme Court in the waning days of his presidency, he did so as part of a broader attempt to strengthen the judiciary. With a Republican president and a Republican Congress waiting in the wings, Adams and his Federalist colleagues looked to the judicial branch as a means of preserving influence after 1801.
The Judiciary Act passed that year was central to this plan: by expanding the federal judicial branch—creating more federal courts and broadening their jurisdiction, funneling more cases into federal rather than state courts—a Federalist-leaning judiciary could exercise influence over the interpretation of law far into the future.
After signing the Judiciary Act in February 1801, Adams rushed the names of the 16 new federal judges through the Senate for confirmation. He also named dozens of new justices of the peace for the city of Washington. The new law had given the president the power to appoint as many of these lower magistrates as he deemed necessary for the growing city. He decided upon 42, signed their commissions, and sealed the letters with instructions that they be delivered.
38 of these letters were delivered, but through some oversight, four weren't. And when Jefferson took office, he instructed his new Secretary of State James Madison not to deliver these "midnight" appointments. Arguing that, since these lower judges didn't enjoy life tenure, he could nullify their appointments, Jefferson announced that he would name his own justices of the peace.
William Marbury and the three other justices of the peace that didn't receive their appointments decided to force Madison's hand—and Jefferson's—by suing to the Supreme Court. They requested a writ of mandamus, a court order demanding that a government official carry out some action—in this case, the delivery of their appointment letters.
For Chief Justice Marshall, the case was filled with opportunity, but also loaded with problems. On the one hand, it offered a chance to make a statement about the power of the Supreme Court. On the other hand, the case pitting Federalist plaintiffs against Republican defendants risked a verdict that would appear narrowly partisan. And while Marshall wanted to strengthen the Court, he also wanted to establish its prestige as a nonpartisan arbiter of law.
Over the preceding several years, the judiciary had become a political battleground. Just as the Federalists had tried to preserve their influence through its expansion, Republicans were trying to weaken it though a series of impeachment proceedings. The two judges the Republicans first went after probably deserved to be removed—one was insane, and both were transparently partisan in their conduct—but Republican efforts were guided more by an interest in establishing a broad power of impeachment than in simply purifying the judiciary.
Within this context, a poorly handled Marbury ruling could easily appear to be just another example of partisan expediency. A ruling by the new Federalist-appointed Chief Justice against the new Republican president, and in support of another recent Federalist appointee, would surely damage the Court's reputation.
As Marshall examined the details of the case, he must have asked himself if there was a way that he could strengthen the Court without appearing partisan. Could he assert the power of the Court against the other branches of government and establish its role as the arbiter of the constitution without provoking further partisan wrangling?
Marshall delivered the Court's opinion in Marbury v. Madison on February 24th, 1803.
He wrote it himself, as he would 24 of the first 26 opinions issued by the Court between 1801 and 1805. He began by arguing that the Marbury case presented the Court with two fundamental questions:
(1) Were Marbury and the others entitled to their commissions?
(2) If so, could the Court provide a remedy?
To the first question, Marshall answered a simple yes. President Adams had signed and sealed their appointments. This completed a legitimate exercise of his executive authority. Simply failing to deliver the commissions didn't constitute a repeal or negation of the appointments.
But the second question, Marshall argued, was more complex. While these appointees were entitled to their commissions, the Court could do nothing to enforce them because it lacked the necessary jurisdiction. Issuing a writ of mandamus fell under the category of original jurisdiction (the area of authority a court has to hear a case the first time it is presented). The other type of jurisdiction was appellate (the authority to rehear a case on appeal when a party believed there was some procedural or substantive error in the first trial).
The problem, Marshall argued, was that while the Supreme Court possessed very broad appellate jurisdiction, its original jurisdiction was severely limited—and it didn't include writs of mandamus. So, the Court couldn't issue one on Marbury's behalf, regardless of the legitimacy of his claim.
Had Marshall's opinion stopped here, the case of Marbury v. Madison wouldn't have been long remembered. But Marshall continued. The confusion inherent in the case, he said, lay in the Judiciary Act of 1789. Passed during the first session of Congress, this act had aimed at fleshing out the very brief terms of Article III of the Constitution. The 1789 act had created a series of lower courts, identified the jurisdictions of the federal and state courts, and provided further details regarding the composition and powers of the Supreme Court.
For example, the act specified that the Supreme Court would consist of a chief justice and five associates. All this was just fine, said Marshall, but the act had also stipulated that the Supreme Court had the power to issue writs of mandamus—and in doing so, Congress had exceeded its authority. The Court's original jurisdiction was explicitly defined by the Constitution, said Marshall, and Congress had no authority to enhance or expand what the Constitution had already determined.
The bottom line: the Supreme Court had no authority to issue the sort of writ Marbury and his friends wanted. Marbury lost. Jefferson and Madison won. Or did they?
In the most immediate sense, the decision in Marbury v. Madison was a Republican victory. The Federalists' attempt to rush through a series of last-minute appointments had partially failed, and the new president couldn't be forced to do their bidding.
But in a broader sense, the ruling accomplished much of what the Federalists had set out to do. For in denying the legality of a portion of the 1789 act, Marshall strengthened the judiciary by asserting the principle of judicial review—the right and power of the Court to rule on the constitutionality of congressional action.
This judicial claim had been debated since 1789. Many argued it was implicit in the language of Article III of the Constitution, which stated that the Court's power extended to "all Cases, in Law and Equity, arising under this Constitution, the Laws of the United States, and Treaties made."
Alexander Hamilton had made the case for this interpretation of the Constitution in Federalist #78. But others argued that the language of the Constitution in this area was vague, and that conceding the power of judicial review would place the judiciary above the legislative branch. Nowhere did the Constitution explicitly grant the Supreme Court the power of judicial review. Moreover, they suggested, it was inconsistent with America's democratic form of government to place so much power in the hands of a tiny group of judges that were appointed to office and enjoyed life tenures.
With their ruling in Marbury v. Madison, the Supreme Court answered a hotly contested question. By asserting the power of judicial review, the Court explicitly claimed for the first time its authority to rule on the constitutionality of legislative acts. For Republicans like Jefferson, this represented a dangerous precedent. But it was difficult to argue the point too aggressively, for should Jefferson have challenged the Court's authority to strike down this congressional act, he would have implicitly defended the authority of the Court to issue the writ Marbury sought—and Secretary of State Madison may have been forced to deliver the appointment letters.
While Jefferson struggled to find a suitable response to Marbury v. Madison, Marshall sealed the deal with another ruling one week later. On March 2nd, 1803, the Court ruled that Congress' repeal of the Judiciary Act of 1801 had been constitutional. The repeal had been pushed by Jefferson and the Republican Congress in 1802 in an effort to undo the Federalist measure.
Federalists challenged the constitutionality of this repeal by arguing that it threatened the independence of the judicial branch. But Marshall said Congress could act in this case, that it did have legal authority to repeal the 1801 Judiciary Act. In other words, by giving Jefferson and the Republicans another small victory, he secured a much larger victory for the power of the Court. By declaring that the Republican Congress had acted constitutionally, Marshall asserted the authority of the Court to act as the arbiter and interpreter of last resort for the Constitution.
John Marshall died in 1835. During his 34 years as Chief Justice of the Supreme Court, the Court would rule on 14 more cases that questioned the constitutionality of congressional action. The Court would affirm the constitutionality of Congress' legislation in all 14.
But with each case, the Court set another brick in the wall of judicial authority. With each affirmation of congressional action, the Court established more forcefully its own power of judicial review.
DNA tests had all but proved what many had long suspected, but just as many had vehemently denied: Thomas Jefferson had a sexual relationship, quite possibly lasting more than a decade, with one of his Black slaves.
So, not knowing what to do, believing that a crisis of epic proportions lay on the horizon, but not seeing anything that could be done to redress this national sin, he surrendered to it and then wallowed in his weakness. He bought and sold slaves and then lamented the degrading impact of slavery on white morals. He lived beyond his means, indulged himself in imported wines and furniture, and then sold away slaves to cover his debts while celebrating the moral clarity of the simple farmer. He used his power as slave-master to maintain a long-term relationship with Sally Hemings and then condemned the despotic behavior of the planter and the lessons in tyranny learned by Southern children.
Thomas Jefferson was a complex man: a deep thinker and a product of the Enlightenment. But when it came to slavery and race, he lost his intellectual bearings. Unable to reconcile his jumble of feelings—his contempt for his slaves, his recognition of the institution's evil, his fears of inevitable conflict, his lust for Sally Hemings—he fell back upon another, very un-Jeffersonian philosophical tradition.
Like the most rigorous of medieval ascetics, or the most anxious of 17th-century Calvinists, he took refuge in the age-old belief in original sin. He traced the history that had enabled slavery to take root and spread until it became the national sin. And telling himself that sin was inescapable, he allowed it to become his own personal sin: evil, miserable, and damning, but an inalienable part of the human, or at least Virginia, condition.
We often link Jefferson with the principle of equality. While Jefferson's Federalist opponents have been branded as social and political elitists—conservatives who insisted that the views of common people must be filtered through the wisdom of the best-bred and educated—Jefferson has been celebrated as the champion of popular wisdom.
And indeed, the central element of Jefferson's republican philosophy was his confidence in the moral judgments of the common man. He believed that all people possessed an intuitive sense of right and wrong, an innate ability to resolve fundamental questions of morality. Jefferson, college-educated, a philosopher and a scientist, even argued that on basic moral questions, a common farmer's moral instincts were the most reliable.
"State a moral case to a ploughman and a professor," he wrote, and "the former will decide it as well, and often better than the latter, because he has not been led astray by artificial rules."
In the final analysis, there was a great deal of coherence to Jefferson's philosophy. His confidence in human reason, his theories of education, and his stoic response to political turmoil were all part of a coherent package. These ideas continue to influence and inspire Americans today.
But the philosophical optimism and creativity that still intrigue us unsettled many of his contemporaries. To Jefferson's critics, his confidence in popular wisdom seemed naive, and his complacent response to political turmoil seemed irresponsible. And so, when he ran for president, his critics challenged not only his policies but also the philosophical temperament that shaped his ideas. He was better suited to teaching than leading, they charged, too speculative and impractical.
And their criticism wasn't entirely unfounded. It's hard to imagine any other politician assuming such a nonchalant response to popular insurrection, much less suggesting that we toss out all our laws and constitution every 19 years.
So, Jefferson's election in 1801 raised questions not just about the content of his thought, but also about the suitability of his temperament.
Could a person of such wide-ranging and speculative intellectual tendencies handle the nitty-gritty demands of politics? Could a philosopher, an intellectual who helped shape many of our most fundamental political and social ideals, translate those ideals into effective policies and actions?
Thomas Jefferson's election to the presidency in 1801 provided an appropriate finale to the political drama of the preceding half decade.
The bitter controversy surrounding the Jay Treaty, the explosive reaction to the XYZ Affair, the assault on civil liberties embodied by the Alien and Sedition Acts, the brawl between Congressmen Lyon and Griswold on the floor of the House...America's first political parties had emerged with a particularly loud partisan bang.
Therefore, when the Electoral College votes cast in December 1800 were counted on February 11th, 1801, and it was revealed that there was a tie for the presidency—not between Jefferson, a Republican, and John Adams, his Federalist opponent, but instead between Jefferson and his Republican running mate, Aaron Burr—the political craziness seemed complete.
For starters, the election had revealed a glitch in the Constitution's presidential selection process. The members of the Electoral College each possessed two votes. They were meant to cast one for their choice for president and one for their vice presidential choice. But these ballots weren't tabulated separately. That is, the presidential and vice presidential elections weren't treated as two separate contests. Instead, both ballots were tossed in the same box, with the first and second place winners serving as president and vice president.
What the constitutional framers had expected was what had occurred four years earlier in 1796: the two most prominent candidates would finish first and second, and serve as president and vice president. In 1796, that meant President John Adams and Vice President Thomas Jefferson. It was—somewhat naively—hoped that, even though the two men had been rivals during the election, they would set aside their differences in true republican fashion in order to serve the common good.
What the Founders didn't anticipate was the formation of political parties that would run presidential and vice presidential candidates as a team. Instead, they'd assumed that the electors' choices would be more diverse, and the likelihood of an entire bloc of electors casting both their ballots for the same two candidates would be a statistical impossibility.
But with the formation of parties and running mates, this was exactly what did occur. And in 1800, the Republican pairing of Jefferson and Burr failed to plan carefully to avoid a tie between them. As Jefferson watched events unfold from his Monticello home, he fumed that "it was badly managed not to have arranged with certainty what seems to have been left to hazard."
But even more grandly, the acquisition of this territory played to Jefferson's vision of an expanding "empire of liberty." While some worried that the vast expanse of Louisiana would prove difficult to govern, Jefferson confidently envisioned the emergence of a series of "sister republics" stretching to the Pacific Ocean.
Perhaps these republics would be part of the United States, perhaps they wouldn't—it made little difference to Jefferson. For united by a common ideology and a shared interest in protecting their republican ideals, these republics would blur the traditional understanding of nationhood and further advance history's progressive course.
One year after securing the Louisiana Purchase, Thomas Jefferson was re-elected to a second term. His first term had been a good one, filled with concrete achievements. In many ways, his first term served to demonstrate that republican ideals could be turned into policy, and that the philosopher could succeed in politics.
What Jefferson refused to acknowledge was that a great deal of his success was only made possible by the very un-Republican achievements of his Federalist predecessors.
Most importantly, his entire program was being financed by the commercial profits made possible by the policies of George Washington and John Adams. When Washington had pushed the Jay Treaty through the Senate in 1795, Jefferson had been outraged. He believed it a humiliating submission to British power, further evidence of Alexander Hamilton's Anglophilic influence. And, he complained, Britain had refused to recognize Americans' rights as neutral shippers; that is, Britain refused to accept the American argument that as a neutral in the conflict between France and Britain, American ships should be allowed to trade freely with both nations.
But in the year following the Jay Treaty, within the improved diplomatic climate, Britain did embrace a relaxed position on neutral carriers—and American ships were allowed to transport both British and French goods without interference. In 1800, Adams negotiated a similar treaty with the French. The result was that, by the time Jefferson became president, the United States was beginning to realize huge profits as a neutral carrier, hauling the cargoes of both warring nations, generating large profits for the American shipping industry, and in the process increasing government revenues collected in American ports.
It was these increasing import tax revenues that allowed Jefferson to pay down the national debt despite the elimination of all other taxes. These same revenues also allowed him to take on a new government expense—the Louisiana Purchase—without breaking the treasury.
On this transaction, moreover, Jefferson had even bigger help. American negotiations with France would have gone much differently had Napoleon not faced such a military crisis in Haiti. Could even New Orleans have been purchased? What price would the United States have had to pay just to access the Mississippi River, much less to acquire vast lands spanning the interior of the continent?
All in all, the jury remained out on Thomas Jefferson at the end of his first term. During his second term, world events would force Jefferson to concentrate on foreign policy. And this time around, fortune would not look so generously on his efforts.
In Thomas Jefferson's second term as president, he set his sights on the acquisition of Florida. Still in the possession of Spain, its acquisition would unfetter American expansion to the south and remove another foreign presence from the continent.
In other words, its acquisition would complete the process begun by the 1803 Louisiana Purchase.
In Jefferson's mind, the two projects—Louisiana and Florida—were united. In fact, it seems likely that Jefferson approached this second-term foreign policy challenge hoping and expecting to repeat the success of his recent Louisiana transaction. Everything just seemed to fall into place in that deal. The gods—or rather, as Jefferson might have put it, the progressive and rational course of history—seemed to be on his side.
The acquisition of Florida represented a slightly different challenge, but why should he not succeed here, as well?
Unfortunately for Jefferson, Spain proved less compliant than France. Florida wasn't particularly valuable to Spain in and of itself. But Spain feared surrendering the peninsula to the United States, placing the expansionist Americans that much closer to much more valuable Spanish holdings in the Caribbean—most importantly, Cuba.
So, Spain refused to deal when Jefferson sent James Monroe to attempt to purchase the territory in 1804.
In the wake of Spain's refusal to deal, Jefferson mulled his options. Military conquest would be relatively easy. Spain couldn't possibly resist an American invasion of Florida. She was, by the turn of the 19th century, a tired old empire and one governed from more than 3,000 miles away. But Napoleon's France, a much more formidable power, was a Spanish ally, and Jefferson worried about how Napoleon might respond to American aggression in Florida.
Therefore, Jefferson also explored a second option. The United States could cozy up to France and try to cut a deal. France was anxious to secure American support in its war with Britain. If the United States pledged its support, perhaps France could convince Spain to sell Florida.
It was a tough call, dependent largely on an even tougher reading of European affairs—or more precisely, a reading of the Napoleonic Wars between France and Britain.
Jefferson pondered these questions through the first half of 1805—and then opted for the military invasion. France would be angry (to say nothing of Spain) but Jefferson believed France needed American ships more than Britain did, and couldn't afford to react too harshly.
Jefferson's reasoning made some sense. But unfortunately for him, just as he readied for the invasion, beginning to mobilize the army and preparing the public for war by publishing anti-Spanish articles in the Republican papers, Britain announced a dramatic change in its maritime policy. Britain's recognition of American neutral shipping rights would terminate as of July 1805. From that point forward, American ships transporting the goods of Britain's enemies should expect to be intercepted by the Royal Navy and their cargoes seized.
This left Jefferson stumped. Here he was about to launch an attack against France just as England signaled a more hostile maritime policy. If not careful, the United States could find itself diplomatically isolated, considered an enemy of both France and Britain.
So, Jefferson changed his mind and his policy. In the fall of 1805, he decided to go with the second option—rather than attacking Florida, he would cozy up to the French, offering them assistance in their war with Britain in return for France's pledge to bring Spain to the table. In the end, it would take until 1819 for Florida to officially become American territory.
In the shorter term, of course, Jefferson's decision was sure to anger the British—but Anglo-American hostilities seemed to be increasing, anyway. And while the French Navy wasn't as strong as that of the British, it could offer the United States some protection on the seas.
Again, Jefferson's reasoning made some sense. But what Jefferson didn't see coming was the Battle of Trafalgar.
On October 21st, 1805, British warships engaged the French and Spanish fleets in one of the largest and most consequential naval battles in history. Roughly 70 ships and 4,000 men clashed off the coast of Spain, and the day ended with the British crushing their enemies. The Spanish armada would never recover, and in the wake of Trafalgar, the French would largely abandon the sea to concentrate on the development of their continental army.
As a result, Britain would "rule the waves" for the next century. It was the worst possible moment for Thomas Jefferson to have just announced a hostile hard-line policy against British maritime harassment.
It's hard to fault Jefferson entirely for his misstep, though. Could he possibly have seen Trafalgar coming? In fact, in the aftermath of the battle, he rushed off a team of high-level diplomats—James Monroe and William Pinkney—to try to patch things up with the British.
Fortunately, the British seemed somewhat conciliatory. They were willing to revise once again their policies on neutral shipping in return for a pledge from the United States that it wouldn't cooperate with French attempts to shut all British goods out of the European continent. Monroe and Pinkney were pleased with that. So, they sent the treaty off to Jefferson, even though they were disappointed that Britain refused to budge on its policies regarding impressment.
The British had for decades, claimed the right to intercept foreign vessels on the high seas, search their crews, and seize British subjects who they judged had deserted from the navy or taken flight in order to evade naval service. This policy of impressment of supposedly fugitive sailors was necessary, the British argued, in order to maintain the strength of their navy—and their navy was Britain's strength.
Perhaps so. But the practice had infuriated Americans for years. It wasn't easy to tell the difference between an English-speaking American and an Englishman in those days, and occasionally, innocent Americans were caught up in these raids and pressed into service in His Majesty's Royal Navy.
Nor did naturalization—becoming an American citizen—protect a British sailor from being forced into service. The British argued that if you were born British, you died British.
But perhaps most offensive to Americans was the disrespect for American sovereignty implicit in the act of boarding American ships by force at sea. After all, wasn't an American ship an extension of the nation, a floating piece of America? How could Britain reasonably claim that it possessed a right of search and seizure at sea that it could not possibly claim on American soil?
When the Monroe-Pinkney Treaty reached Jefferson's desk, he rejected it outright.
Britain's dogged insistence on a right to intercept American ships and impress sailors was too great a violation of his understanding of American autonomy, and too flagrant a violation of the independence-minded Spirit of '76. To submit would be to accept American subordination to Britain, a modified form of the colonial subservience that Americans had thrown off 30 years before.
Philosophically speaking, Jefferson was likely correct. But his decision to reject the treaty carried huge economic and practical costs. Trade with Britain represented more than two-thirds of all American commerce. Furthermore, the relatively small additional trade directed toward the European continent was all but controlled by the British Navy. This meant that virtually all of America's overseas commerce was jeopardized by the rejection of the treaty negotiated by Monroe and Pinkney.
Jefferson understood this, but he was willing to risk commercial wellbeing as the price of defending a principle. In the final analysis, he was willing to accept no trade over trade that degraded the United States. He was willing to risk commercial collapse rather than submit to a commercial agreement that would have compromised what he perceived to be a fundamental American principle.
Therefore, with Britain now even more hostile than before, and with French markets largely shut off by the British Navy, Jefferson played his last remaining card: an embargo.
By taking American ships completely off the sea, they wouldn't be placed at risk of capture—and America wouldn't be forced into war by some avoidable naval confrontation. In addition, he believed that the total suspension of American commerce would force both Britain and France to adopt more rational maritime policies.
So, in December 1807, Congress passed, at Jefferson's urging, an embargo on all foreign commerce. American ships would only be allowed to engage in the coastal trade, so they were barred from sailing for foreign ports.
As with every other foreign policy decision made during Jefferson's second term, there was a logic to this one. And consistent with his entire presidency, this logic was informed by Jefferson's ideals.
In fact, in Jefferson's rhetoric of 1807, we can hear the old Jefferson, the Jefferson of 1776, resuming his campaign against America's old oppressor.
But this new battle wouldn't be nearly as successful as the first. The British economy proved far too resilient to be pressured by Jefferson's embargo. British warehouses were already full of the cotton and wheat they most needed from America, allowing Britain to survive the blockage of American trade, at least for the short term. And just about the time these reserves began to run out, cracks in Napoleon's continental blockade opened up new markets for Britain in Spain.
To make matters worse, while the British economy proved almost invulnerable to embargo, the American economy wasn't. New England, a region heavily dependent on foreign shipping, was hit particularly hard. In Boston, ships sat idle in the harbor while unemployed sailors roamed the streets. Merchants, bankers, and dockworkers all felt the pinch. The fact that New England had been the stronghold of the Federalist Party—and had always opposed Jefferson—didn't make any of this go down more easily.
In fact, as the embargo-induced recession grew worse, New Englanders resorted to outright evasion and resistance. A steady stream of goods started to flow up the Hudson River into Canada for export from ports beyond the control of American customs officials. Ships sailing from Boston to Charleston, engaged in the legal coastal trade, managed to "blow off course" with amazing regularity, allowing them to trade illegally in West Indies. On the floor of the Massachusetts state legislature, there was talk of nullification—the highly contested claim that a state had a right to cancel or ignore a federal law. In the streets of New England towns, people even talked of seceding from the union.
As this evasion and resistance grew stronger, Jefferson's patience waned.
And so, in 1808, the man who had once said a "little rebellion now and then" was a good thing declared the Hudson River region to be in a state of insurrection and sent in the military to curb the illegal trade.
The philosopher who had once warned against the slippery slope of governmental power urged Congress to pass an enforcement act to increase the authority of customs officials to seize "suspicious" cargoes without warrants. The republican ideologue who once had proclaimed confidence in the people to regulate their own behavior and argued that national emergencies should be met by a citizen army rising to defend its shared interest, now requested from Congress an army of 30,000 men to aid in the suppression of the insurrection that he believed threatened the national interest.
In December 1808, James Madison was elected president. But to a large extent, he'd already assumed direction of Jefferson's administration.
As Jefferson's embargo failed to secure any British concessions, as New England's resistance grew more concerted and flagrant, and as Jefferson's response to this revolt grew more strident, the president also grew more removed. He'd always suffered from severe migraines. In the last year of his presidency, these conspired with the pressures of his failed policy to force Jefferson largely into the background. By the time Madison was inaugurated in March 1809, Jefferson was no longer the central figure in his own administration, much less the city of Washington.
Congress made the point when it voted to repeal his embargo in the waning days of his presidency—and set the date for its expiration to coincide with his departure from office.
On March 4th, 1809, James Madison was inaugurated president. The confrontation with Britain over its maritime policies would continue for several years, culminating in the War of 1812. But Jefferson would watch all of this from the distance of his Virginia estate. He beat a hasty retreat back to Monticello as soon as the burdens of office were removed from his shoulders, never again returning to Washington.
Instead he spent the rest of life tending his gardens, collecting books, and planning the University of Virginia—the project most dear to the philosopher's heart and perhaps better suited to his temperament.