After Darnley was murdered, Bothwell was a prime suspect - it was absolute madness for Mary to marry him.
I have heard several theories:
1] Mary loved Bothwell, and had for years, so she married him regardless of the consqeuences
2] Bothwell captured and raped Mary, forcing her to marry him
3] Bothwell captured Mary and wooed her over a short period of time
4] Mary had porphyria, and her decision was influenced by 'madness' . . .
At the moment, I'm really not sure which answer is right!