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Grant had attended a cabinet meeting on April 14th, and Lincoln had invited Grant and his wife to the theater, but the Grants decided instead to travel to Philadelphia. After Lincoln was shot, Secretary of War Edwin Stanton got a message to Grant about the President's death and summoned him to Washington. The following day, Grant wanted to order the arrest of paroled Confederate officers, but Major General Edward Ord convinced Grant to reverse this decision.
Grant attended Lincoln's funeral on April 19, where he wept openly. He said of Lincoln, "he was incontestably the greatest man I have ever known." He did not look forward to having Andrew Johnson as President and told his wife Julia, "Reconstruction has been set back no telling how far."
Later that month, General William Tecumseh Sherman had, without consulting Washington, concluded an agreement with Confederate General Joseph E. Johnston to effect the latter's surrender, on generous terms that he believed Lincoln would have approved of, based on Lincoln's conversation with Sherman at City Point. Secretary of War Stanton considered the terms to be much too lenient and criticized Sherman. Grant agreed, but was conflicted because of his loyalty for his close friend Sherman. Grant handled the matter diplomatically and was able to instruct Sherman to renegotiate the agreement consistent with the terms set at Appomattox.
In May 1865, the Union League of Philadelphia purchased a house for the Grants in that city. Grant commuted for a time between Philadelphia and Washington, return home on the weekends, but he and Julia moved to Washington that October. For political purposes Grant declared his legal residence to be in Galena, Illinois. On July 25, 1866, Congress promoted Grant to the newly created rank of General of the Army of the United States.
According to his biographers, such as H. W. Brands, Grant was the most popular man in the country. When President Johnson argued with Congress over Reconstruction, he tried to his case to the people with a series of speeches on the road. Johnson sought to capitalize on Grant's popularity by having Grant travel with him. Ever the good soldier, Grant agreed to go with Johnson, but privately he told his wife that he thought Johnson's speeches were a "national disgrace". Grant presented appearances of support for Johnson, while trying not to offend Republican legislators. It was called the "Swing Around the Circle" and below is a rare photograph from one of these events.
Johnson realized that Grant would be a potential candidate in the 1868 presidential election. He considered replacing Secretary of War Stanton with either Grant or Sherman. Grant discussed the matter with Sherman and convinced him to avoid the politically troubled president.
After the speaking tour, Johnson sent Grant on a fact-finding mission to the South. Grant filed a report recommending continuation of the Freedmen's Bureau, a federal agency that was set up to help freed slaves. Johnson opposed this. Grant did not believe the people of the recently defeated South were ready for self-rule, and thought they required further U.S. military occupation. He warned of threats by disaffected poor people, black and white. However he agreed with Johnson that Congress should allow representatives from the South to be seated in Congress.
In 1866, John Lee Chapman, Maryland's governor, Thomas Swann, a Johnson supporter, threatened to remove Baltimore Police Commissioners and appoint his own. The existing commissioners were politically alligned with Radical Republicans. The Mayor of Baltimore, Radical John Lee Chapman, wanted troops sent in to prevent a riot. Grant was reluctant to send federal troops into a loyal state. Instead he traveled to the city himself and mediated a settlement that would allow both groups' poll watchers to make sure there would be fair elections.
More conflict between Radicals and Conservatives over the Reconstruction of the South was on the horizon. Congress passed the Reconstruction Acts which divided the southern states into five military districts run by the army to set up protection for the freedmen's rights. Military governers general were to lead transitional state governments in each district. Grant was to select the general to govern each district. He preferred Congress's plan to the President's. One of these generals, Phillip Sheridan, removed public officials in Louisiana who impeded Reconstruction. Displeased with this, Johnson sought Sheridan's removal. Grant recommended a rebuke, but not a dismissal. Throughout this period, the U.S. military protected the rights of more than 1,500 African-Americans elected to political offices.
After the Civil War, thousands of Irish veterans joined the Fenian Brotherhood whose intention was to invade and hold Canada hostage in exchange for Irish independence. In June 1866, Johnson sent Grant to Buffalo, New York, to assess the situation. He ordered the Canadian border closed to prevent Fenian soldiers from crossing over. In June 1866, the United States Army arrested 700 Fenian troops at Buffalo, and the Fenians gave up on their plan to invade Canada.
President Johnson had wanted to replace Secretary of War Stanton, who sympathized with Congressional Reconstruction. Johnson asked Grant to take the post. Grant recommended against the move. Congress had passed the Tenure of Office Act, which required Senate approval of any removal of a cabinet appointment. Johnson forced the issue by making it an interim appointment during a Senate recess. Grant reluctantly agreed to accept the post temporarily. When the Senate reconvened, it reinstated Stanton. Johnson requested that Grant refuse to surrender the office to Stanton and let the courts resolve the matter, but Grant stepped aside, much to Johnson's consternation. On January 14, 1868, newspapers friendly to Johnson published a series of articles seeking to discredit Grant over his return of the War Department to Stanton. Grant defended himself in a letter to the President, which became public. This increased Grant's popularity. Grant took no role in the later impeachment proceedings against Johnson.
In 1868 the Republicans chose Grant as their presidential candidate on the first ballot at the Republican National Convention in Chicago. In his letter of acceptance to the party, Grant concluded by stating "Let us have peace," which became his campaign slogan. As was common practice at the time, Grant remained at his home in Galena during the campaign, and left most of the active campaigning and speaking on his behalf to his campaign manager William E. Chandler and other "surrogates".
The Democrats nominated former New York Governor Horatio Seymour. The Democrats' campaign focused mainly on ending Reconstruction and returning control of the South to the former ruling class. This alienated many War Democrats in the North. Democrats also tried to remind voters of Grant's reputation as "Grant the Butcher" during the overland campaign. But in the election that year, Grant won by 300,000 votes out of 5,716,082 votes cast. In the electoral college, Grant won 214 votes to Seymour's 80.
When he assumed the presidency, Grant had never before held elected office and, at the age of forty-six, was the youngest person elected president up to that time. Grant was the first president elected after the nation had outlawed slavery and had granted citizenship to former slaves. Implementation of these new rights would be slow to come.