There were many different things that challenged the new government between 1789 and 1800. Different things such as Foreign Affairs and new rules that were established such as the Alien and Sedition Acts. All of these things some how changed the government and the views of the citizens of the United States.
During the rise of John Adams elections, he came across a rival with France. The French believed that during Jay's Treaty, the French - American Alliance betrayed them by joining forces with the British. The French eventually decided to seize many American merchantmen that were traveling to England. Once Adams heard about this event, many of his fellow members of his political party urged him to declare war. Instead of war, Adams chose to negotiate by sending three men to Paris to discuss the men being seized on the ships. This did not work out so an undeclared "naval war" broke out for two ongoing years. In the midst of those two years, John Adams discovered that a new French government was welcoming an American ambassador/minister resident without bribe money. Adams sent three men over to Paris and both sides decided to forget the 1778 Treaty and work out their problems with peace. This action challenged the governments views forever because they did not know whether negotiating or war would be the better solution overall. .
Another challenge that the government faced was the Alien and Sedition Acts. These rules stated that the residence requirement for American citizenship would be five to fourteen years, the president had the power in peacetime to order any alien out of the country, the Alien Enemies Act permitted the President in wartime to jail aliens at his pleasure and any one guilty of sedition, speaking or writing with intent to defame the president or other members of the government, would be fined or jailed. These new laws affected the refugees of France because they were deciding whether or not it would be better to leave the country or stay.