Confederate General Henry H. Sibley, in command of the Army of New Mexico, had issued a proclamation taking possession of New Mexico in the name of the Confederate States on December 20, 1861, calling on the citizens to abandon their allegiance to the Union and to join the Confederacy, warning that those "who co-operate with the enemy will be treated accordingly, and must be prepared to share their fate."

In February 1862, Sibley advances northward from Fort Thorn up the valley of the Rio Grande, toward the territorial capital of Santa Fe and the Union storehouses at Fort Union.

Along the way, Sibley detaches fifty-four men to occupy Tucson.

The Confederate advance follows the west bank of the river via Fort Craig, which is garrisoned by a thirty-eight hundred-man Union force under Colonel Edward Canby.

Knowing he cannot leave such a large Union force behind him as he advances, Sibley attempts to lure the Union forces out into battle on favorable terms.

On February 19, Sibley camps at the sandhills east of the fort with the intention of cutting the Union lines of communications with Santa Fe.

The Union forces advance from the fort on February 20 but are hit with heavy Confederate artillery and are forced to retreat.

The Confederates march to Valverde Ford, six miles (nine point seven kilometers) north of the fort, in an attempt to outflank the Union forces he next day.

Canby attacks, but the Union forces are driven back by the Confederates under Colonel Thomas Green, who takes command after Sibley is indisposed (some say of drunkenness).

Canby's forces retreat to Fort Craig but refuse to surrender.

Poor hunting grounds remain for the Dakota after their cession of lands east of the Red and Big Sioux Rivers in Minnesota and Iowa; they have become increasingly hostile to white settlers and traders, many of whom encroach on Indian territory and are unscrupulous in their dealings.

When 1862 arrives shortly after a failed crop the year before and a winter starvation, the federal payment is late.

The local traders will not issue any more credit to the Santee and the lead trader trader, Andrew Myrick, goes so far as to tell them that they are 'free to eat grass or their own dung'.

As a result, the Dakota War of 1862 begins when a few Santee men murder a white farmer and most of his family on August 17, 1862, igniting further attacks on white settlements along the Minnesota River.

The Santee now attack the trading post, and Myrick is later found among the dead with his mouth stuffed full of grass.

A band of warriors under Chief Little Crow ambushes and destroys an army detachment from Fort Ridgely, near New Ulm, on the upper Minnesota River, then besiege the heavily defended fort itself, on August 20.

Dakota warriors decide not to attack Fort Ridgely, and instead turn to the settlement of New Ulm, killing white settlers on August 24, 1862.

The Dakota have created panic in Minnesota by their barn-burning, slaughter of men, women and children, and destruction of crops but, due to the Civil War, repeated appeals for help are required before President Lincoln appoints General John Pope to assemble troops from the Third and Fourth Minnesota Regiments to quell the violence.

Minnesota Governor Alexander Ramsey also instructs Colonel Henry Sibley (the state's first governor) to aid in the effort.

Sibley raises a volunteer militia force at Fort Snelling and sets out to punish the Sioux.

At Wood Lake, Sibley decisively defeats Little Crow (September 23, 1862), who escapes westward. (Returning the next year, he will be shot dead by a Minnesota farmer for the bounty on Sioux.)

Three hundred and three Santee captives are convicted of murder and rape by military tribunals and sentenced to death on November 5, six weeks after the Battle of Wood Lake.

Some trials last less than five minutes, and the Dakotas have no one to explain the proceedings to them or to represent them.

Most of the convicted Santee have their sentences commuted after President Lincoln reviews the trial records and distinguishes between those who had engaged in warfare against the United States and those who had committed the crimes of rape or murder of civilians, but thirty-eight are hanged on December 26, 1862, in the largest mass execution in U.S. history.

Meanwhile, a large military operation is begun by Sibley in cooperation with Brigadier General Alfred Sully.

Some Dakota refugees and warriors had made their way to Lakota lands following their expulsion from Minnesota.

Battles continue between the forces of the Department of the Northwest and combined Lakota and Dakota forces.

Colonel Henry H. Sibley with two thousand men had pursued the Sioux into Dakota Territory.

Sibley's army defeats the Lakota and Dakota in the Battle of Big Mound on July 24, 1863; the Battle of Dead Buffalo Lake on July 26, 1863; and the Battle of Stony Lake on July 28, 1863.