How can one atone for the sin of fornication, and will God forgive this sin and accept prayers? What should be done if this relationship results in a pregnancy of unknown paternity, especially with the suspicion of semen entering the womb despite external ejaculation?

Your regret for committing adultery is a condition for the validity of your repentance. If you are sincere in your repentance, Allah will accept it: "And indeed, I am Forgiving to whoever repents, believes, and does righteousness, and then is guided." The woman's pregnancy does not affect the validity of your repentance or the acceptance of your prayers. The child is not attributed to you, but to its mother. Devote yourself to the betterment of your religion and worldly life, and do not preoccupy yourself with her matter.