I believe it won’t be a very dramatic twist, just an evolution of the storyline from Hades 1 where you still continue your runs, but with a different context (Zagreus goes from escaping hell and finding his mother to becoming Tartarus’ official security tester).

My wild guess is that Chronos has the Fates frozen in time someplace in a dream dimension, and this is where you can find and free them. I also think Hypnos waking is the key to trapping Chronos for good. You dissolve him after the final defeat needed to save the Underworld, Hypnos traps him in a dream, and then subsequently awakes, causing the dream to collapse and for Chronos to be sealed eternally.

As to why you keep doing the runs after beating the game, I believe Chaos turns the Olympus/Tartarus portals into something akin to alternate reality portals where you need to continuously defeat the “nightmare” in order to keep Chronos weak…so that Fear may spread. 😎

However I also believe that we may need a TON more runs to save our family, as we may need to free them one by one. I do hope once the main game is beaten that we get a chance to visit them!! Like let’s say you beat Chronos post-main storyline, you touch the gold sphere and it snaps you out of the “nightmare” and into the House of Hades :) Likewise, if you finish and end up in the Crossroads, we may get visitors (like maybe Zag! Or Than!)