Nick Spencer's Amazing Spider-Man run has been extremely hit-and-miss, but there's no denying that the Kindred mystery has been a compelling one. In the writer's final, giant-sized issue, we learn that Sarah and Gabriel Stacy were Kindred, working at the behest of the A.I. that Harry Osborn left behind after his death in Spectacular Spider-Man #200.
Things get a little muddled, but the Harry who returned at the start of "Brand New Day" was just a clone, and the real Harry's soul has been stuck in Hell this entire time. The cloned Harry dies protecting his father and, with that, he's back on the shelf...or grave (the real deal's soul was freed by Mephisto, but he's presumably in the Marvel Universe's version of Heaven now).
Gabriel and Sarah die after the disease that rapidly ages them finally takes its toll, leaving Spidey the victor. As for Mephisto, it's confirmed that he took Peter Parker and Mary Jane's marriage in order to stop their daughter from being born, as he foresaw the one who will end his reign in Hell.
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So, Spencer attempted to make some sense out of "One More Day," but doesn't retcon it and never bothers having Peter propose to MJ (despite teasing it his entire run). They're still together, so it's possible Mephisto will target them again, but the best thing to come out of the whole "Kindred Saga" was seemingly "Sins Past" being retconned.
We have a lot of unanswered questions, but whether they'll ever be addressed remains to be seen; was Harry controlling Gabriel and Stacy from Hell? It looked that way, but this all quickly devolves into being as nonsensical as how Spencer brought Steve Rogers back in Secret Empire.
Check out Harry's sacrifice and a big Spider-Girl tease from Amazing Spider-Man #74 below: