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Chapter 1 begins before the revival; they're estranged as a couple and living in separate homes.
This story covers 2013 - My Struggle 2 in Spring 2016. There are some time jumps between present and past as we look through the history of what their lives were like after they were driven apart by the very thing that brought them together.
Over the course of the season 10 timeline, Mulder and Scully have to heal, forgive and learn to trust again as they decide what the future holds for their relationship before it's too late.
Time was an illusion, God was dead. So were they, for all intents and purposes.