Some Republicans wanted to do away with the judiciary and in 1801 they controlled the executive and Congress while Federalists still controlled the judiciary.
Many Americans had never trusted the judiciary due to its history in colonial America where judges were always dependent on the Crown even while the judiciary in England had gained independence following the Glorious Revolution.
The judiciary was never really viewed as an independent entity during colonial times as judges, or magistrates as they were often called, carried out executive and administrative functions.
As a result, many state constitutions sought to limit this judiciary dependence on the executive and instead make the judiciary dependent on the people by making their terms limited and allowing for removal of judges often with just a simple majority in the legislature.
With judges having to interpret different sources of law they often exercised a great degree of indoemdemce in applying the different laws to their rulings and lawyers were often seen as people who just manipulated the different laws to their benefit.
To fix this issue reformers sought to codify the laws — relying on statutes rather than unwritten common law.
Starting in 1776 many states began to do away with English common laws that did not apply to their needs and codify the ones that did but by the 1780s many had realized that this created too confusing of a legal environment and many leading Americans began pushing for an independent judiciary.
The Constitution brought about an independent federal judicial system but many states at this time still retained dependent judiciaries.
Anti-Federalists had favored a federal judicial system that allowed for only a Supreme Court at the federal level and other federal cases being tried in existing state courts whereas Federalists favored a federal judicial system that could override state courts.
The Constitution, in Article III, put off many of the contentious specifics of the federal judicial system to the future and the following Judiciary Act of 1789 created a three tiered federal judicial system with the Supreme Court at the top, then circuit courts, and the district courts at the bottom.
Anti-Federalist fears of a federal judicial system ignoring common law rights were largely alleviated by amendments that would make up the Bill of Rights being enacted almost simultaneously.
It was common for judges to be appointed not based off of legal expertise but based off of political considerations and that stayed the case immediately after the Constitution.
As an example John Jay was appointed chief justice by Washington and had only served as chief justice of New York for a few weeks and of the 28 men who judges in federal district courts in the 1790s only eight had held similar judicial positions in their states but nearly all were important political figures.
Because many judges had their positions due to their political importance many viewed their roles as political and exercised their political influence, wrote political articles, gave politically charged instructions to grand juries, etc.
More specific examples include Jay serving simultaneously as Secretary of State (when Jefferson was coming back from France) and chief justice as well as Congress assigning duties to the Supreme Court which included conducting the census.
One hope of Federalists with the federal courts was that they could be used as an instrument to reduce loyalties Americans had to their individual states and this was attempted to be accomplished in its operations (the Judiciary Act was written so they initial filings of federal cases would most likely end up in federal trial courts instead of state courts) as well as rulings (like Hylton v. United States that confirmed the federal government’s right to a broad tax power).
Federalists also argued that the federal courts could punish crimes using criminal common law even if not federal criminal statutes existed which would expand the power of the federal courts and frightened the Republicans who viewed this as a means for the courts to essentially act as a legislative body.
When Federalists lost the election of 1800 they sought to expand the federal judiciary even more; with a Jefferson taking office in March 1801 and the new Republican Congress not being seated until December 1801 the lame-duck Congress passed a new judiciary act.
Supreme Court justices no longer had circuit court duty and six new circuit courts were created; the jurisdiction of circuit courts were expanded; common law crimes were recognized as being the remit of the federal courts; and the Supreme Court was reduced to only five justices from six thus Jefferson wouldn’t be able to appoint someone to the Supreme Court until two vacancies had happened.
Additionally, Adams appointed several justices to the federal bench including John Marshall as chief justice as well as appointed numerous other Federalists to newly created judicial positions on the eve of Jefferson’s inauguration.
When Republicans took power after the 1800 election they focused on undoing the changes the Federalists had made to the federal judicial system.
The 1801 Judiciary Act was repealed and Republicans focused on impeaching Federalist judges.
In 1804 the House impeached and the Senate convicted John Pickering who was a federal district court judge in New Hampshire and the house also passed a resolution to impeach justice Samuel Chase.
Chase, however, was not convicted as many Republicans viewed his politicking as something not abnormal for a judge and didn’t see him as having broken any actual laws.
Struggle between Federalists and Republicans over the future of the judicial system didn’t just take place at the federal level but also in the individual states as well.
Most illustrative case was in Pennsylvania which foreshadowed the eventual splitting of the Republicans into different factions where moderate Republicans sought to maintain an independent judiciary over fears of more democratic factions becoming overzealous after initial cooperation between the two sides over judicial reform.