Congress
Lyon was an unsuccessful candidate for election to the Second and Third Congresses. He unsuccessfully contested the election of Israel Smith to the Fourth Congress. Lyon won election as a Democratic-Republican to the Fifth and Sixth Congresses (March 4, 1797 – March 3, 1801); he was not a candidate for renomination in 1800.
Lyon had the distinction of being one of the first two members investigated for a supposed violation of House rules when he was accused of "gross indecency" for spitting in Roger Griswold's face; Griswold was investigated for attacking Lyon in retaliation.
On January 30, 1798, the House was considering whether to remove William Blount of Tennessee from office. Griswold was trying to attract Lyon's attention in order to have a dialogue on the issue, but Lyon was ignoring him on purpose, since they belonged to opposing political parties (Lyon was a Democratic-Republican and Griswold a Federalist). Griswold finally lost his temper and insulted Lyon by calling him a scoundrel, which at the time was considered profanity. Their clash escalated when Lyon declared himself willing to fight for the interest of the common man. Mockingly, Griswold asked if Lyon would be using his wooden sword, a reference to Lyon's supposed dismissal from Gates' command during the Revolution. Furious, Lyon spat tobacco juice on Griswold, earning himself the nickname "The Spitting Lyon".
Lyon later apologized to the House as a whole, claiming he had not known it was in session when he confronted Griswold, and meant no breach of decorum or disrespect to the body; he also provided a written letter of apology. Not satisfied with the apology, on February 15, 1798, Griswold retaliated by attacking Lyon with a wooden cane, beating him about the head and shoulders in view of other representatives on the House floor. Lyon retreated to a fire pit and defended himself with the tongs until other Congressmen broke up the fight, with several pulling Griswold by his legs to get him to let go of Lyon. Although the committee appointed to investigate recommended censure of both Lyon and Griswold, the House as a whole rejected the motion. The issue was resolved when both Lyon and Griswold promised the House that they would keep the peace and remain on good behavior.
Lyon also has the distinction of being the only person to be elected to Congress while in jail. On October 10, 1798, he was found guilty of violating the Alien and Sedition Acts, which prohibited malicious writing about the American government as a whole, or of the houses of Congress, or of the president. During the Quasi War with France, Lyon was the first person to be put to trial for violating the acts after he published editorials criticizing Federalist President John Adams.
Lyon had launched his own newspaper, The Scourge of Aristocracy and Repository of Important Political Truth, when the Rutland Herald refused to publish his writings. On October 1, Lyon printed an editorial which included charges that Adams had an "unbounded thirst for ridiculous pomp, foolish adulation, and selfish avarice," as well as the accusation that Adams had corrupted the Christian religion to further his war aims. Before the Alien and Sedition Acts had been passed, Lyon had also written a letter to Alden Spooner, the publisher of the Vermont Journal. In this letter, which Lyon wrote in response to criticism in the Journal, Lyon called the president "bullying," and the Senate's responses "stupid."
Once the Alien and Sedition Acts were passed, the Federalists pushed for this letter to be printed in the Vermont Journal, which Spooner did, thus adding additional charges against Lyon. One other charge included publishing letters written by the poet Joel Barlow, which Lyon had read at political rallies. These also were published prior to the Acts. Lyon's defense was to be the unconstitutionality of the Acts, as Jeffersonians saw them as violating the First Amendment to the Constitution. In Lyon's particular case, there was the aforementioned letter to Alden Spooner as well as that of Barlow, which meant Lyon felt entitled to bring up the Constitution's safeguards against ex post facto laws. This defense was not allowed.
Lyon was sentenced to four months in a 16 by 12 feet (4.9 m × 3.7 m) jail cell used for felons, counterfeiters, thieves, and runaway slaves in Vergennes, and ordered to pay a $1,000 fine and court costs (equivalent to $19,355 in 2025); Judge William Paterson lamented being unable to give a harsher punishment. A bit of a resistance movement was created; the Green Mountain Boys even threatened to destroy the jail and might have done so if not for Lyon's urging peaceful resistance. While in jail, Lyon won election to the Sixth Congress by nearly doubling the votes of his closest adversary, 4,576 to 2,444. Upon his release, Lyon exclaimed to a crowd of supporters: "I am on my way to Philadelphia!"
After years of effort by his heirs, in 1840 Congress passed a bill authorizing a refund of the fine Lyon incurred under the Alien and Sedition Acts and other expenses he accrued as the result of his imprisonment, plus interest.
In the election of 1800, the vote went to the House of Representatives because of a tie in electoral votes between Thomas Jefferson and Aaron Burr, who were supposed to have been the Democratic-Republican candidates for president and vice president respectively. Many Federalists decided Burr as president was preferable to Jefferson.
House members voted by state, with a majority required for a state's vote to be awarded, and a majority of nine states required to win. During the first 35 ballots, Jefferson carried eight states and Burr six, with two states counted as "no result" because of a tie among their House members. Vermont was one of the two "no result" states, because Lewis Morris voted for Burr and Lyon cast his ballot for Jefferson. On the 36th ballot, several Federalists decided to break the impasse by allowing the election of Jefferson through either casting blank ballots or absenting themselves from the House chamber during the vote. Morris was among the Federalists who took part; as a result of Morris's decision to be absent, Lyon's vote for Jefferson moved Vermont into his column. Vermont was one of two states to switch from "no result" to Jefferson, and he carried 10 states on the final ballot; Lyon thus played an important role in Jefferson's victory.