Vader didn't get turned into toast on Mustafar and defeated Obi-Wan, taking him prisoner, but Padmé and her children are still gone (maybe she died and there was no one to get her to the med station fast enough, causing the babies to die with her, or she managed to flee with her ship).
Vader and the Emperor are both pissed off, because dammit, they really would've liked some very-strong-in-the-Force children to train as the next Sith. How lucky for them that they just so happen to have a prisoner who might not be the Chosen One but is very strong in the Force and therefor might even be the better option for producing Force-strong children than Padmé who wasn't notably Force sensitive.

So, Vaderkin raping and impregnating Obi-Wan. (which is possible due to whatever machinations you want: always-a-female!Obi-Wan, human physiology is different for Stewjon natives, Sith alchemy, etc)

Optional bonus points for: Sidious doesn't necessarily participate in the sex, but he does like to watch