The truth of the Scotius/Jean/Werner triangle is revealed in 1602 #8. After escorting Virgina Dare back to her home village in America, Scotius and Werner have a private conversation. Scotius apologises to him.
Scotius: “You see...You did not know Jean was...That is to say, you...you allowed her disguise to fool you...You thought her a man. I...if Jean was anyone’s, she was mine. She would have been mine. And...I thought that you were in love with her. I was jealous of you, and jealous of her...And all that time, you thought her a man. So. I was a fool. A jealous, witless fool. And I...With all my heart, I apologise.”
Werner in return says that he should be the one apologising to Scotius.
Werner: “I was truly deceived, and thought that Jean Grey was a man. But I do believe I was in love with that young man.”
Previous: 1602 #7
(Please note that I did not set out to give a summary of 1602. If you want to know the outcome, you can source for other sites purely dedicated to 1602, or check out this limited series comics in 8 parts.)