It is in 1602 #3 where Gaiman establishes the relationship between Scotius and Jean. Scotius catches Werner and Jean having an early morning chat up in a tree. A seemingly jealous Scotius interrupts the pair to inform them that they should get dressed for their morning prayers in the chapel. Scotius also informs Jean that he “shall talk to [her] later”.
Here it is evident that Gaiman is playing out the original love triangle of Scott/Jean/Warren in the 60s, but with a twist, revealed later in the series. In the chapel, Javier is at the altar praying. Seated to his left are Jean and Scotius (who keeps a watchful eye on her), and to Javier’s right, the rest of the team.