Star caused the Stapocalypse.
I've been suspecting this since the beginning (Stapocalypse, Star, star-shaped portal...). Star, upset over Jam apparently winning the titular "ship war" and being berated by her mother for airing her family's dirt, ends up snapping, deciding "Fine, then let me be a screw-up", If I Can't Have You…, or a combination of the two and using her magic to unleash Lucitor on Earth. Given that she's the most powerful member of the family since Queen Eclipsa, this won't end well...- Another possibility, after Toffee ended up possessing Moon instead of Ludo and even learned of his canon fate in this AU, could be that he'll find a way possess Star through her wand and, in doing so, be the cause of the Stapocalypse.
Elizabeth and Jam end up both existing simultaneously in a new timeline when Jackie and Star decide to share Marco.
As is pointed out elsewhere, Jackie has no ill will towards Star and both of them are clearly important to Marco. So Elizabeth and Jam could end up transplanted into a new timeline where they can coexist but have their original memories intact. Elizabeth and Jam end up both existing simultaneously in a new timeline when Jackie asks Marco to be the sperm donor for her child.
Since Chloe can't impregnate her herself. Eclipsa will attempt to convince Star and her friends to turn against the MHC.
She's managed to earn Jackie's sympathy, but not her cooperation. Eclipsa, with the All-Seeing Eye, would know the kind of people Star, Marco, and co. are; well-intentioned individuals with more morals than the MHC and Glossaryck. To try to turn them against her enemies, she could potentially try to convince them to help her with her revenge. But being who they are, won't, even if they have sympathy.