Burr earned his dubious reputation not so much from the duel which killed Alexander Hamilton as from his involvement in the Essex Junto which planned to lead New England out of the United States, and also his involvement in a plot to build a personal empire on the west side of the Mississippi River.
The Essex Junto consisted of a group of fundamentalist Federalists who saw the acquisition of Louisiana as the death knell of the Federalist Party. They knew the new territory would soon evolve into states whose inhabitants, mostly farmers and Jeffersonians, would support Jefferson's Democratic Republican party. The plan was to have Burr elected Governor of New York after which New York would lead other states in a secession movement. The Junto only fell apart when Hamilton discovered it, and described Burr as
a dangerous man and one who should not be trusted with the reins of Government
Newspapers printed the story and Burr lost support. It was then that he challenged Hamilton to a duel during which Hamilton was killed. This ended Burr's political career, although he remained Vice President of the United States and presided over the Senate even though he was under indictment for murder in New York and New Jersey.
Burr stayed in Spanish Floriida until the uproar over Hamilton's death subsided, and while there developed a scheme with one James Wilkerson to have Louisiana secede from the Union and build a personal empire for themselves. The plan only failed because Wilkerson lost his nerve and revealed the plan to Jefferson. Burr attempted again to flee to Florida but was intercepted and tried for treason. He was acquitted, largely because of the rulings of the presiding Judge, John Marshall. Even so, his several attempts to break the country apart have led to his designation as the "assassin of liberty."
An excellent resource you might consider is Fallen Founder: The Life of Aaron Burr by Nancy Isenberg