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Who is "Dad"?Edit
Ingame it serves as a hint system for any missing Gravestones that the player hasn't yet picked up.
Though it could be possibly related to Halley's father, Edward, there's also a more likely possibility it could belong to Yuri's father, Jinpachiro - who resides in his son's soul, The Graveyard, keeping the power of the Seraphic Radiance at bay - contacting his son to assist him in mastering his fusion powers.
Time Traveller Immunity - Averting a ParadoxEdit
A time paradox can be averted by considering Yuri dead and the good ending of Shadow Hearts a result of a second timeline where Karin replaced Anne as the new mother of the second Yuri: the future has changed, and the timeline where Covenant happened got erased and a new future was created.
The first timeline's Anne wasn't Karin, but just a normal Russian woman (as shown by the fact that her element is Light, not Fire like Karin). When Yuri and Karin travel back in time at the end of Covenant, Ben falls in love with Karin instead of Anne and creates a second Yuri, different from the first one, changing the future timeline. In this alternate future, Karin does everything Anne did in the first timeline (because she took Anne's role) and Covenant never happens.
Possibly, the scene of the soul being raised from the Mistletoe tree means that Yuri's memories were sent back in time to the second Yuri, who now knows what would happen if he doesn't defeat the Four Masks.
Using the Time Travel Immunity Theory to avert this paradox, it can be argued that Saki only sees a resemblance between Yuri and Karin, instead of being aware that Karin would become Yuri's mother, because in the timeline where Covenant takes place, Karin is not Yuri's mother to begin with. A Russian woman is. Saki's "prediction" might not be an actual prediction, but just her being worried that Karin might travel in time because she's aware of Kato's plan. If the TTIT is applied, then Karin is not Kurando's aunt.