When the government of Virginia, through statewide referendum, decided to secede in a landslide majority Lincoln threw his support behind an unsanctioned minority rump convention in the northwest extremity of the state and declared it to be the legitimate government of all of Virginia. When it became clear that he could not sustain that absurdity, he let them break away from the state and form their own government over their counties plus a couple dozen more to the south who got dragged along unwillingly. That state is now called West Virginia.
In Missouri Lincoln decided one day that the sitting state government, though it was unionist and showing no signs of seceding anytime soon, wasn't unionist enough for his tastes (meaning it was reluctant to go to war and to provide him with militias to invade other states). So he called in the federal army and sent it to attack the capitol, causing the governor, liuetenant governor and state legislature to flee for their lives to the southwest. After they were out of the way he simply appointed a military dictator to run Missouri for the next four years.
In Maryland there were some indications that the state government would either tilt toward secession or say something critical of Lincoln's war policy. Lincoln's response? Round up all the legislators, mayors, and other elected officials who weren't enthusiastic enough about his war mongering and throw them in Fort McHenry's prison.