Madison learned from his defeat from the first time he ran for elective office, and campaigned for votes. He made it very clear that he supported a Bill of Rights, and opposed a new Constitutional Convention, which he believed would be the "End of Days," so-to-speak. Madison garnered 1,308 votes to Monroe's 972; Baptists and Lutherans rallied to Madison's side, due to his stance on free exercise of religion, but also for his support of a Bill of Rights. On 30 April, 1789, George Washington took the Oath of Office as the first President, and soon thereafter Madison was sworn in as a member of the House of Representatives. Once sworn in, Madison wanted to get the Bill of Rights added to the Constitution as soon as possible.
Two of his twelve proposed rights were defeated. The first was a proposal that wanted to force the state governments to honor the rights of citizens; that would eventually become the 14th Amendment. Among the reasons why that proposal was defeated was that many pointed out that it seemed inconsistent with Madison's argument in Federalist Paper No. 45 during the Ratification debate. The other one that was defeated wanted to be sure that members of Congress couldn't vote themselves a raise during their term in office - that proposal would become the 27th Amendment. Members of Congress also made their preference clear that the Bill of Rights should be listed at the end of the Constitution; Madison envisioned that they would be embedded within the appropriate Articles.
There was no magical reason why the Bill of Rights are in the order they are listed; it was merely the order that was in Madison's draft based on how his brain operated. Once the ten Bill of Rights were ratified, Madison became a "Secular Moses" in Congress, and the ratification of the first ten amendments also killed opposition to the Constitution. As Brookhiser stated, the Constitution (with the Bill of Rights) had "A Thousand Fathers", but Madison was it midwife.
Madison labored hard in pushing Thomas Jefferson to become Washington's SecState, and he initially supported Alexander Hamilton as SecTreas. While Hamilton was flat-out bursting to be the Secretary of the Treasury (no one else was even remotely close to his abilities, and he knew it), Jefferson played hard-to-get. While it was the tradition to be "reluctant" to hold office (the behavior was modeled after Cincinnatus in Rome), Washington became tired of the act, and Madison had to convince Jefferson to basically "get over himself." Finally, in 1790, Jefferson was confirmed as the nation's first Secretary of State, and Washington's first Cabinet was complete (including SecWar Henry Knox, and Attorney General Edmund Randolph).
President Washington's "team" started to fragment early, due to Hamilton's proposed Economic Plan. Hamilton first wanted to repay the foreign and domestic debt incurred from the Revolutionary War. Hamilton knew that the U.S. needed to make good on its foreign debt in order to be able to effectively trade and to have a good credit rating abroad. Hamilton also wanted to repay the domestic debt (calling it "Assumption") by having the federal government "assume" the state debts, which would not only increase the trust in the new government from the citizens, but would also mean that states would become beholden to the national government. This was the moment that Madison aligned himself as an opponent to his former ally, mostly due to his belief that Hamilton's plan extended the sphere of influence of the national government at the expense of the states - it was the genesis of the debate on how to interpret the Constitution.
Very soon after that compromise, Hamilton unveiled his plan for a National Bank. Hamilton viewed repaying the foreign and domestic debts as a short-term strategy, but he saw the National Bank as a long-term safeguard for the nation's economic future Hamilton wanted twenty percent of the National Bank start-up capital to come from customs duties and tax receipts, with the remaining eighty percent from investors, who would have a (in)vested interest in the success of the institution. Hamilton's vision of a National Bank that largely controlled the flow of money and the liquidity of assets stirred up a hornet's nest of opposition, with Madison leading the charge.
Hamilton's argument that the bank was authorized due to the "Necessary and Proper" clause in the Constitution did not resonate with Madison (or Jefferson). For political reasons, Madison had become a "Strict Constructionist" in terms of interpreting the Constitution. We can tell that politics (the art of who has the power to make the rules) motivated Madison to oppose Hamilton, because in Federalist #44, authored by Madison, he argued that the "Necessary and Proper" clause was not only valid, it was good government.
In 1791, Congress rejected Madison's claim that the National Bank was unconstitutional, and although Washington signed the National Bank into law, he (behind the scenes) had secured his flank by having Madison write a veto statement, just in case he was of a mind to do so. The "Political Score" so far by 1791: Hamilton, 1.5, and Madison/Jefferson 0.5, with Hamilton securing a clear victory with the National Bank.
In 1789, the French Revolution started with the Fall of the Bastille, and that conflict started to affect American politics in 1791. Madison & Jefferson believed it was necessary to fully support France; to them it was de facto payback for losing to Alexander Hamilton on the National Bank. Madison and Jefferson had no intention of creating and organizing a political party, yet it happened in 1791. Both disliked factions, but they never admitted to themselves (based on their letters, etc.) that they were in fact partisan politicians.
In 1791, Madison AND Jefferson traveled north in order to recruit Aaron Burr (New York) to their camp - who better to challenge Hamilton in his home state than Burr, who had worked with and opposed Hamilton over the years . . . they seemed to be creating an Anti-Hamilton League of Extraordinary Gentlemen. During their trip north, Madison and Jefferson found political disciples and "worker bees", such as Philip Frenau and his newspaper, The Gazette. Using Frenau's newspaper in 1791, Madison espoused his long-term views of what would secure America's future, in direct opposition to Hamilton. Agrarian over Industrial, and Self-Sufficiency over Markets were the Madison and Jefferson watchwords of the day (only Madison, as President, will see the error of these politics), countering Hamilton's very influential "Report on Manufactures."
Madison introduced something new in political theory in the early-1790s: public opinion and its role in government. Madison came to believe in more than "popular choice" (voting); people should be "partners" in government as well. This was a key development, in that in the not-too-distant future, Madison would prevail against at Hamilton, in part due to Hamilton's rigid belief that only a small talented elite should be involved in the business of government. It was this new political theory that allowed Madison to create a political party that he and Jefferson would call Republicans in 1792, and their party would have far more voters than the opposing party, the Federalists, by the late-1790s.
In January of 1792 the King of France, Louis XVI, was beheaded, and in February, Great Britain declared war on France. As a leading Francophile and Republican, Madison was thrilled with the events unfolding in France; unfortunately, Madison (and Jefferson) often denied or excused the massacres and atrocities that were common in that revolution. What existed of the French Government sent Charles Genet to America as the chief diplomat in charge of securing American assistance in helping them in their war, using the Treaty of Alliance (1778) from the Revolutionary War as the legal framework. Washington issued his neutrality stance, and Madison saw the policy as Anti-French. Madison's and Jefferson's political party, the Republicans (with Genet's help), used their newspapers to attack not only Washington's policy, but Washington himself. The mistake that Madison, Jefferson, and Genet made was that Washington was far more popular in America than the far-off French Revolution . . . Madison discovered that there were limits to what public opinion could accomplish, especially if he tried to manufacture / inflate public opinion.
Madison didn't believe that an excise tax was a good enough reason for a revolution. Not only that, but he also believed that the actions of a minority were a threat to the majority - he viewed the rebellion in much the same way as did Washington & Hamilton, but offering his support would not be good politics. It must have galled Madison to no end to see that the Federalists linked the rebellion to the many "Democratic Societies" that had sprouted up in America (groups of Republicans meeting in homes, for example); Madison saw them as using public opinion against his own party. It was the Federalists that scored another huge win against the Republicans when Washington peacefully ended the conflict, in part by offering amnesty to the rebels. All the while, Madison kept looking for any political leverage or advantage to use against the Federalists in 1794 - it must have seemed to Madison that the Federalists still held most of the cards . . .
The Jay Treaty, negotiated in 1794, and ratified in 1795, all in secret, became public in the Summer of 1795. Alexander Hamilton strongly supported the treaty (he was the main reason why it was narrowly ratified), and although the Republicans thought Jay sold-out the United States, Madison was reluctant to engage in a "Word-War" with Alexander Hamilton again. The partisan politics over the Jay Treaty is what finally ended the connection between Madison and Washington (it had been steadily declining since 1792, when the Republican party was established). On 30 April, 1796, the House of Representatives voted 51-48 to appropriate money to put the Jay Treaty in effect. Over twenty Republicans flipped, and voted for the appropriation - it was official, in political terms - James Madison had become damaged goods.
Jefferson actually wrote a rather nice letter to John Adams after the results of the election were made official, but before he sent it to Adams, he sent it to Madison for some feedback. Madison convinced Jefferson that he should not sent the letter, in that it would be disloyal to his supporters, and the Federalist President John Adams would soon attack Jefferson anyway. In short, Jefferson had tried to reach across party lines, but Madison nixed it. In the same spirit, John Adams actually thought about appointing Madison as the Minister Plenipotentiary to France, and contacted Madison feeling him out in terms of the posting. Madison made it clear to President-Elect Adams that he would not accept the position, doing so for political reasons. To Madison, it seemed counterintuitive and counterproductive for a Republican help a Federalist President.
At about the same time, Hamilton was taken down by the Republican political machinery, but not by Madison; by that time, Albert Gallatin (who would become an absolute historical superstar during the Presidencies of Jefferson, Madison, and Monroe) was the leader of the party. Under Gallatin's leadership, and using the newspaper controlled by James Callendar (the "Pitbull Publisher" of the Republicans), the "Reynolds Affair" was resurrected, and Hamilton lost favor with many Americans, regardless of party, with his out-of-proportion defense of his actions.
The initial reaction to the resolutions was overwhelmingly negative; Madison and Jefferson were way-out on a political limb, but the Federalists broke ranks and over-reacted. The Federalists enforced the Sedition Act to the point where they actually lost political support across the nation. The over-reaching by the Federalists resulted in a political goldmine for the Republicans, and James Madison was able to begin his political comeback, winning election to the Virginia Assembly in 1799, the same year that George Washington died. James Madison claimed that Republicans were the real defenders of liberty (back then, liberty was defined as state's rights), and the Federalists, in their zeal to destroy the opposing party, wound up being the Republicans' best friend.