The Civil War erupted in 1861 and lasted four grueling years.  During the war, against the advice of his cabinet,
Lincoln signed  the Emancipation Proclamation that freed  the slaves. The  Republicans of the day worked to pass 
the Thirteenth Amendment, which outlawed slavery, the  Fourteenth, which guaranteed equal protection under the
laws, and the Fifteenth, which helped secure voting rights for African-Americans.

"Jefferson Davis, passionate advocate of slavery and states-rights, was a leader of the Democrats in the U.S. Senate; he had also been Secretary of War under President Pierce. When Mississippi withdrew from the U.S. in 1861 he left the Senate and was chosen President of the Confederacy by the Confederate Congress two weeks later.

The Democratic Party was the party of the Confederacy. Yet it did not entirely disappear in the north: in the election of 1864 its candidate General McClellan received 45% of the popular vote (Confederate states did not vote). This may have been a more of a reflection of how unpopular the Civil War was; George Brinton McClellan was the peace (with a continuation of slavery) candidate, and at the time a Northern victory looked unlikely.

The triumph of the north in the Civil War changed many things, but it did not change the Democratic Party. With former Confederacy soldiers not allowed to hold office (as per the 14th Amendment), or even prohibited from voting (Reconstruction Acts of 1867) and newly enfranchised former slaves allowed to vote (15th Amendment), the South was briefly Republican. In fact former slaves had rights only in areas where they were protected by federal soldiers. In the north a few corrupt Democratic urban "machines," dependent on the spoils of office, and pro-slavery northern Copperheads, survived; victory pushed many former northern Democrats into the Republican Party.

The re-emergence of the Democratic Party in the South was engineered by the Ku Klux Klan and allied individuals. By preventing former slaves (not surprisingly, they were all Republicans) from voting, and with the restoration of the right of former Confederate soldiers to vote and hold office, by 1872 the Democratic Party was restored to power in the South."William P. Meyers;   http://www.mcn.org/e/iii/demhist.htm

Clinton Pardons on final day in office

Clinton issued 140 pardons on his last day of office (January 20, 2001).  Clinton  issued 395  pardons  duting his two-term presidency.

Some controversial pardons include the following:

• Carlos A. Vignali had his sentence for cocaine trafficking commuted, after serving 6 of 15 years in federal prison.
• Almon Glenn Braswell was pardoned of his mail fraud and perjury convictions, even while a federal investigation was underway regarding additional money laundering and tax evasion charges.^[11] Braswell and Carlos Vignali each paid approximately $200,000 to Hillary Clinton's brother, Hugh Rodham, to represent their respective cases for clemency. Hugh Rodham returned the payments after they were disclosed to the public. Braswell would later invoke the Fifth Amendment at a Senate Committee hearing in 2001, when questioned about allegations of his having systematically defrauded senior citizens of millions of dollars.
• Marc Rich, a fugitive, was pardoned of tax evasion, after clemency pleas from Israeli prime minister Ehud Barak, among many other international luminaries. Denise Rich, Marc's former wife, was a close friend of the Clintons and had made substantial donations to both Clinton's library and Hillary's Senate campaign. Several months after her last donation, emails reveal Republican attorney "Scooter" Libby asked her to approach Clinton about pardoning Marc Rich. Clinton agreed to a pardon that required Marc Rich to pay a $100,000,000 fine before he could return to the United States. According to Paul Volcker's independent investigation of Iraqi Oil-for-Food kickback schemes, Marc Rich was a middleman for several suspect Iraqi oil deals involving over 4 million barrels of oil.
• Susan McDougal, who had already completed her sentence, was pardoned for her role in the Whitewater scandal; McDougal had served 18 months on contempt charges for refusing to testify about Clinton's role.
• Dan Rostenkowski, a former Democratic Congressman convicted in the Congressional Post Office Scandal
• Melvin J. Reynolds, a Democratic Congressman from Illinois, who was convicted of bank fraud, 12 counts of sexual assault, obstruction of justice, and solicitation of child pornography.
• Roger Clinton, the president's half-brother, on drug charges. Roger Clinton would be charged with drunk driving and disorderly conduct in an unrelated incident within a year of the pardon. He was also briefly alleged to have been utilized in lobbying for the Braswell pardon, among others.

It has been pointed out that the total number of pardons Clinton granted was comparable to other presidents and that Republican lame duck presidential pardons have also been controversial, including President George H. W. Bush's pardons of six Reagan administration officials accused or convicted in connection with the Iran-Contra affair and Orlando Bosch.