The case stemmed from a trial by a military commission of Lambdin P. Milligan, Stephen Horsey, William A. Bowles, and Andrew Humphreys that convened at Indianapolis on October 21, 1864.

The two judges who reviewed Milligan's petition disagreed about the issue of whether the U.S. Constitution prohibited civilians from being tried by a military commission and passed the case to the U.S. Supreme Court.

During the American Civil War, the administration of President Abraham Lincoln dealt with Union dissenters by declaring martial law; sanctioning arbitrary arrest and detention; suspending the writ of habeas corpus, which requires justification of any detention; and initiating trials by military commission rather than in conventional civil courts.

The rationale for these actions was that Article 1, Section 9 of the U.S. Constitution authorizes the suspension of the writ of habeas corpus "when in Cases of Rebellion or Invasion the public Safety may require it".

Clement Vallandigham, an Ohio politician and antiwar Democrat, was placed under arrest on May 5, 1863, taken to Cincinnati for a trial before a military commission, and jailed.

The commission considered five charges against the men: conspiracy against the U.S. government, offering aid and comfort to the Confederates, inciting insurrections, "disloyal practices", and "violation of the laws of war".

[12][13] The defendants were alleged to have established a secret organization that planned to liberate Confederate soldiers from Union prisoner-of-war camps in Illinois, Indiana, and Ohio, and then seize an arsenal, provide the freed prisoners with arms, raise an armed force to incite a general insurrection, and join with the Confederates to invade Indiana, Illinois, and Kentucky and make war on the government of the United States.

Efforts were made to secure pardons for Milligan, Bowles, and Horsey, with the decision passing to President Johnson following Lincoln's assassination.

[15][16] On May 10, 1865, Jonathan W. Gorden, Milligan's legal counsel, filed a petition for a writ of habeas corpus in the Circuit Court of the United States for the District of Indiana in Indianapolis.

[15] Milligan's petition alleged that a federal grand jury had met in Indianapolis during January 1865, which it did, and it had not indicted him, which is also true, making him eligible for a release from prison under the congressional act.

Among the members of Milligan's legal team were Joseph E. McDonald; David Dudley Field, who was a New York lawyer and brother of U.S. Supreme Court justice Stephen Johnson Field; James A. Garfield, a member of Congress in his first ever courtroom argument and a future U.S. president;[21] and Jeremiah S. Black, who had been former President James Buchanan's U.S. Attorney General and U.S. Secretary of State.

[18][20] On April 3, 1866, Chief Justice Salmon P. Chase handed down the Court's decision, which decreed that the writ of habeas corpus could be issued based on the congressional act of March 3, 1863; the military commission did not have the jurisdiction to try and sentence Milligan; and he was entitled to a discharge.

[20][22] Under the U.S. Constitution this included security against unreasonable search and seizure, a warrant for probable cause before arrest, and if indicted, a speedy trial by jury.

[23] The majority opinion further observed that during the suspension of the writ of habeas corpus, citizens may only be detained without charges, not "tried" or executed under the jurisdictions of military tribunals.

President Lincoln had suspended the writ nationwide on September 24, 1862,[25] and Congress had ratified this action on March 3, 1863, with the Habeas Corpus Suspension Act.

Chief Justice Chase noted that, in the South, "courts might be open and undisturbed in the execution of their functions, and yet wholly incompetent to avert threatened danger, or to punish, with adequate promptitude and certainty, the guilty conspirators".

The first of these may be called jurisdiction under MILITARY LAW, and is found in acts of Congress prescribing rules and articles of war, or otherwise providing for the government of the national forces; the second may be distinguished as MILITARY GOVERNMENT, superseding, as far as may be deemed expedient, the local law and exercised by the military commander under the direction of the President, with the express or implied sanction of Congress, while the third may be denominated MARTIAL LAW PROPER, and is called into action by Congress, or temporarily, when the action of Congress cannot be invited, and, in the case of justifying or excusing peril, by the President, in times of insurrection or invasion or of civil or foreign war, within districts or localities where ordinary law no longer adequately secures public safety and private rights.

"[29][30] Justices David Davis and four others (Nathan Clifford, Stephen Johnson Field, Robert Cooper Grier, and Samuel Nelson) signed the majority opinion.

[26][33] However, as Justice Davis described the status of the Circuit Court of Indiana at the time, "It needed no bayonets to protect it, and required no military aid to execute its judgments".

[34][24] Ex parte Milligan became well known as the leading U.S. Supreme Court case that found the president exceeded his legal powers to suppress dissenters during the American Civil War.