There is an element from a story set during that universe's second World War, which plays into the modern story. It involves a reveal that needs the story in the past to play out in order for the modern day reveal to work.
To be honest, I've driven myself a little loopy trying to shoe-horn both arcs into the series in a way that works, and I have never been happy with the solutions that I've come up with.
One idea, and something which I think may address the problems, is to run the arc as a mini-series. I'm putting together the idea with this in mind, and beginning to think about possible artists who might work - thus allowing Jonathan to come back onto the main series and build the modern day universe, but build in the necessary back story to make the latter reveal work.
The arc was always going to be called The Theatre of War, so for now that would be the working title of the mini-series.
Watch this space...