There were two factions in the fledgling Republican Party: The Radical Republicans and the Moderate Republicans. The Radical Republicans were anti-slavery, some passionately so. The Moderate Republicans, aligned with Abraham Lincoln, wanted to preserve the Union. For them the issue of slavery was peripheral.
In 1864, the Radical Republicans were so opposed to Abraham Lincoln that they put forward their own candidate, General John C. Fremont, for president. 
The Radicals had planned to kidnap Lincoln, hide him, then bring fake impeachment charges against him. But when Lincoln was re-elected (thanks in part to General W.T. Sherman capturing Atlanta) the kidnap plot of the Radicals mutated: now the President, the Vice President (Andrew Johnson) and the Secretary of State (William Seward) were all to be kidnapped and control of the Executive branch of government was to be seized. 
Another angle of attack was via the Washburne Committee, which held hearings concerning “cotton passes” being issued. Headed by Illinois congressman Elihu B. Washburne (Radical Republican) in January through early February 1865, the investigation was thwarted when Lincoln refused to hand over lists of persons for whom he had signed cotton passes. A partial list was finally obtained through Hansen Risley of the Treasury Department but the sought-for names of Ward Lamon and Orville Hickman Browning, friends of Lincoln, were not therein. It was an “all the President’s men” situation: What did Lincoln know, and when did he know it? But without the names of Lamon and Browning having been revealed, the Washburne Committee adjourned. A new method of attack was then sought. 
The big crisis came when on April 6, 1865, at City Point (now Hopewell, Virginia), General Godfrey Weitzel was authorized by Abraham Lincoln to give permission to the “gentlemen who had acted as the Legislature of Virginia in support of the Rebellion” to convene. Edwin Stanton greatly feared this would set a precedent for other of the Rebel legislatures to reconvene and be recognized. Stanton, subordinate of the President, countermanded his boss’s order. Unless a Reconstruction plan including occupation by Union Army soldiers was implemented, Stanton, head of the War Department, would have been sidelined and his importance diminished in peacetime. 
About 100 years after Lincoln’s death, Dr. Ray Neff, a health sciences professor at Indiana State University with a chemistry background, de-ciphered coded messages left by Colonel Lafayette Baker, Union spymaster.  A relevant portion of the deciphered messages includes…
On the thirteenth he [Edwin Stanton] discovered that the President had ordered that the Legislature of Virginia be allowed to assemble to withdraw that state’s troops from action against the U.S. He [Stanton] fermented immediately into an insane tyrade [sic]. Then for the first time I realised his mental disunity and his insane and fanatical hatred for the President. There are few in the War Department that respect the President or his strategy, but there are not many who would countermand an order that the President had given. However, during that insane moment, he sent a telegram to Gen. Weitzel countermanding the President’s order of the twelfth.  (Baker may have gotten the exact dates wrong.)
Said Stanton to Major Thomas Eckert after countermanding Lincoln’s order, “If he [Lincoln] would know who rescinded his order – we will let Lucifer tell him. Be off, Tom, and see to the arrangements.”  
“There were at least eleven members of Congress involved in the plot,” revealed Baker’s decoded message, “no less than twelve Army officers, three Naval officers and at least twenty four civilians, of which one was a governor of a loyal state. Five were bankers of great repute, three were nationally known newspapermen and eleven were industrialists of great repute and wealth.” 
Shortly before he “died” in 1868 at the age of 41, Colonel Baker was seen to be writing in a book. One William Carter inquired, “But, General, them books is already wrote.” And he said, “Right, they are going to have to get up early to get ahead of old Lafe Baker.” And then he laughed. In sworn testimony Carter recalled, “I picked up one of the books and looked at it, and I saw that he was writing cipher in it.” 
President Andrew Johnson nominated Baker for appointment to the grade of brigadier general of volunteers, April 26, 1865, but the United States Senate never confirmed the appointment.  That likely explains why William Carter calls Baker “General” in the above. Contrary to accepted history, Colonel Baker did not die in 1868. In an article published in the Idaho State Journal (Pocatello, Idaho), on November 4, 1977, Vaughan Shelton claimed that Colonel Baker faked his “death” in 1868 and assumed a new identity: R.D. Watson of Fulton County, Kentucky. (Background: Escape Of Lafayette Baker, Ersjdamoo’s Blog, July 18, 2015.)
The inner workings of Republican assassins caused Abraham Lincoln to be murdered on April 14, 1865. However one Edward Steers, Jr. claims that the Confederate government, not a faction of the Republican Party, was behind the assassination of Abraham Lincoln.  The Steers theory however makes less sense than that of an intra-Republican Party coup d’état. The Confederates killing the easy-going Lincoln would have meant for them a harsher Yankee government and even their leaders being hanged for treason. The assassination of Abraham Lincoln worked to the South’s disadvantage when tough Reconstruction policies were implemented. Cui bono? (To whom the benefit?). The benefit was not to the South but to Radical Republicans as well as to others. (See also: Blowback From Intra-Party Coup d’état, Ersjdamoo’s Blog, July 17, 2015.)
——- Sources ——-
 The Lincoln Conspiracy, by David Balsiger and Charles E. Sellier, Jr. Los Angeles: Schick Sunn Classic Productions, 1977.
 “Escape Of Lafayette Baker”, Ersjdamoo’s Blog, July 18, 2015. https://ersjdamoo.wordpress.com/2015/07/18/escape-of-lafayette-baker/
 “Ray Neff Discovers Coded Messages”, http://uts.cc.utexas.edu/~wbova/fn/history/lincoln_02.htm
 “Lafayette C. Baker”, Wikipedia, July 23, 2015.
 “Edward Steers, Jr.”, Wikipedia, July 23, 2015.