Bill Cipher, after being destroyed in Stanley's mind, woke up back in his own dimension- the mindscape. He was weak- it would take years for him to regain his strength.. But he waited.
Bill was lonely, all his friends were leaving him because he failed to take over the world.. He wanted some one to care for, some one who would look up to him and always be by his side. He figured it was time for him to bare the next generation of his kind. Being a demon, he was basically both genders- but that didn't stop him from getting his own child. He didn't want to love some one, he hated almost every one- he just had to use some one..
He knew no one would have the ability to carry such a powerful baby demon with lots of energy- so he had to play the part of a mother- oh wait, the child doesn't have to know. Bill's plan was to become a single father, and take his next plot to rule the world- father and son.. Or daughter.