The use of the pen name of Mark Twain first occurred in Samuel Clemens's writing while in the Nevada Territory which he had journeyed to with his brother.Carolyn Grattan Eichin, "From Sam Clemens to Mark Twain; Sanitizing the Western Experience, " Mark Twain Annual, Vol 12, 2014, 113. Clemens/Twain lived in Nevada from 1861 to 1864, and visited the area twice after leaving. Historians such as Peter Messent see Clemens's time in Nevada as "the third major formative period of Mark Twain's career" (after his time in Hannibal and upon the Mississippi) due to his encounters with "writers and humorists who would both shape and put the finishing touches on his literary art." The Routledge Encyclopedia of Mark Twain states that despite the few "disagreeable experiences" he had there, Twain "thrived in Nevada." Among those things he learned was "how far he could push a joke", a lesson learned from some "disagreeable experiences" he brought upon himself.

Arrival Having deserted the Marion Rangers (a small band of Confederate irregulars) due to a dislike of military life, Samuel Clemens was ready for a clean break with his past. He had lived in St. Louis for two weeks when he decided to accept his brother's offer that would provide this fresh start.

Samuel's brother Orion Clemens (who "had moved toward the position that slavery was morally wrong") had stumped for the presidential ticket of Abraham Lincoln in northern Missouri during the election of 1860 alongside St. Louis lawyer Edward Bates (whose law offices Orion had worked in during the 1840s). Lincoln made Bates his attorney general, and Bates recommended Orion to Secretary of State William H. Seward for a political appointment. This suggestion was accepted, and Orion was nominated by Lincoln to be secretary of the Nevada Territory on March 23, 1861 and was confirmed by the Senate on March 27, 1861. Despite a generous salary, no funds to relocate to Nevada were provided, and without the means to move, Orion struck a deal with Samuel that if he paid for their journey he would serve as Orion's private secretary. It was under this agreement that Samuel and Orion Clemens left for Carson City, Nevada on July 18, 1861 on an overland stagecoach leaving from St. Joseph, Missouri that would take 19 days to arrive. Each ticket was $150 (a month's wages from Orion's new job), Samuel paid the sum with money saved from when he was a riverboat pilot. The population of Carson City at the time was 2,000.

Despite the fact that the Nevada Directory for 1861-62 listed Samuel Clemens with the prestigious title of assistant secretary of state, the job could not maintain his interest. He felt that there was not enough writing in the job to keep both his brother and him busy. He also bristled at being underneath Orion's authority referring to him in his letters as "his majesty the Secretary".

Lingering Southern sympathies Samuel Clemens before the Civil War had considered joining the Know Nothings but joined the Constitutional Unionists made up of ex-Whigs who supported the Dred Scott decision (and won the majority of Southern border states in the election of 1860).

Historian Arthur G. Pettit points out that "Clemens rejected even the moderate Democratic candidate Stephen Douglas, who carried Clemens's own state. Clemens's Southernism, in other words, was a matter of conscious choice as well as regional background." Before the war Clemens held the Whig ideal of having both Union and slavery, but as things progressed he did not have any problem with the idea that states could secede if they felt aggrieved.

Pettit relates that, after Clemens's unhappy time in the irregular militia, he was glad to set out for Nevada rather "than to be at once a disloyal Northerner and a treasonous Southerner." Historian Louis J. Budd states that Clemens was hardly alone in escaping the war in this manner: "In fleeing west with his brother, Sam had plenty of company as, throughout the war years, many thousands of able-bodied men crossed the plains in the same direction."

Arriving in Nevada did not force Clemens to alter his convictions. While the territory was "aggressively dominated by Union men", there was a loud and well-organized Southern minority whose stronghold was in Virginia City (which had been named by Southerners). These supporters for Nevada secession even claimed victory in defeating a statehood proposal because it would allow entry to free blacks – calling the bills defeat the "slaughter of that free nigger Constitution". As time went on, and the war began to shift for the benefit of Union forces, the weight of popular opinion did as well, and Samuel Clemens soon had to take stock of where he stood on the matter.

Mining

After seeing silver ore emerge from one of the mills of the Comstock Lode, Samuel Clemens (tired of working under his brother) began to spend much of his time in the mining districts of Humboldt and Esmeralda. Some of the towns he had an extended connection with include Aurora and Unionville, Nevada (which had originally been named Dixie but had its name changed in 1861 after a close vote). In these areas, Clemens engaged in prospecting and working as a pocket miner with dreams of striking it rich. Clemens, working with an investment made by his brother Orion, took up several partners. Most notably was a partnership with Calvin Higbie (to whom the book Roughing It would be dedicated) and Robert Howland.

Despite great dreams of success, none of Clemens' efforts were overly successful. The rush of immigration to strip the area of silver had been ongoing since the spring of 1859, and Clemens' attempt to strike it rich was very late. By the time he began mining, amateur efforts to strike it rich were hardly viable, value of shares in mining outfits was beginning to collapse from over speculation, and lawyers mitigating disputes were viewed as the only ones sure to make a fortune.

In Roughing It, his stories about his time in Nevada and the West, Clemens and Higbe find a vein of silver that will make them millionaires and fill out the paperwork to make a legal claim, but they both get distracted and fail to do the upkeep necessary to keep the claim valid, and others are able to take it over and make fortunes. Historian R. Kent Rasmussen notes that there was a promising claim that the partners lost in 1862, and "Though their lost claim later proved valuable, it would not necessarily have made the men millionaires." Rasmussen holds that "He magnified the episode enormously" for comic effect.

Having found quartz-mining in search of silver difficult, and not finding enough to support himself, Clemens began working in a quartz mill shoveling tailings for small wages. He was unhappy with the work.

Correspondent

In February 1862, Samuel Clemens began to send occasional letters to the major paper in the Nevada Territory, the Virginia City Daily Territorial Enterprise. By July, he was asking Orion if he could assist him in finding a job as a correspondent. In the fall, he was offered $25 per week to become the city editor of the Enterprise. The offer to be an editor was more than he had anticipated, and he worried about his "inexperience and consequent unfitness for the position." Having been self-sufficient since he was 13 and worrying about falling into debt, Clemens accepted the job despite his worries.

The Territorial Enterprise was run by its founding editor Joseph T. Goodman who mentored Clemens in his new role as editor. Goodman and his staff had enjoyed Clemens's letters that he had signed as "Josh", especially one that satirized the oratory of the territory's chief justice. It also may have seemed advantageous to employ someone with connections to the government. Clemens began covering "vice, the mines, ghost stories, social functions, and other intrigues (sometimes imaginary) in his local columns" for the Enterprise. By December 1862, he was reporting on the territorial legislature and courts in Carson City.

One of his more popular pieces in 1862 was the unsigned "Petrified Man" in which Clemens claimed that a petrified man who had lived "close about a century ago" had been found "south of Gravelly Ford." Historian Bruce Michelson concludes Twain used this hoax to both ridicule the local politician Sewall and mock a public who through gullibility were too quick to accept a mass of petrification reports. The humorous story quickly was picked up by other newspapers and spread east.

In a letter dated February 3, 1863 to the Territorial Enterprise from Carson City, complaining about a lavish party that kept him "awake for forty-eight hours" Clemens signed his work "yours dreamily, MARK TWAIN", the first use of the name under which he would become famous. In May–June 1863, Twain made his first visit to San Francisco, travelling with Clement Rice – eating and drinking throughout the city and making important literary connections. He visited again, alone, in September. During this time, Twain often got his letters re-published in papers throughout the region, and near the end of 1863, began contributing to The Golden Era, a San Francisco literary journal.

Shifting sympathies When Clemens came to Virginia City, he began boasting that he had been a first lieutenant in the regular Confederate Army. It was soon found out that he had been merely a second lieutenant in a self-organized militia of Missouri farm boys. Because of this boast, Clemens offended people on both side of the issue, including his brother's boss, Territorial Governor James W. Nye, who called him a "damned secessionist." Humboldt County judge G.T. Sewall swore he would whip Clemens for his sympathies if he ran across him. In a letter to his friend William H. Clagett, Clemens complained of the news that "they" (Union troops) had "thrashed" and defeated "our Missourians".

Clemens's behavior became an increasing embarrassment to his steadfastly loyal Republican brother Orion, as Samuel was seen as a disloyal troublemaker who spent too much time in saloons. Samuel Clemens's attitude began to change in 1862 as the general opinion became more heavily Union when the Northern armies began winning more battles. Clemens began to hedge his Confederate sympathies, and then abandoned them outright. By September 1862, in his letters to Clagett, he began to refer to the Union soldiers as "we".

The scrapbook Clemens kept while in Nevada initially was filled with newspaper articles that hailed secessionist opinions in the West, but by the end of 1862 he began pasting in editorials of leading citizens demanding that Orion purge the government of anyone with Southern sympathies. (Orion did fire a probate judge and notary public for this reason.) Samuel Clemens continued to collect articles about the results of people who expressed Southern sympathies that had just months before been tolerated. In July 1863, after a flag earlier planted on Mt. Davidson by Union supporters (to overlook Virginia City and mock its Southern sympathizers) survived an intense electrical storm, Clemens, now writing under his penname Mark Twain, presented its survival through the lightning strikes as a mystical omen of Union victory. With this, Twain publicly had shown his newly undivided devotion to the Union. He also portrayed an incident in San Francisco as an omen for the fall of the Confederate cause when all the lights suddenly went out at a meeting of Copperheads (Northern Democrats calling for immediate peace). Twain would go on to protest a clause in a proposed Nevada constitution to disfranchise any that voluntarily bore arms for the Confederacy, claiming that, even in his Missouri days, he always had an underlying affection for the Union.