The Walking Dead shed some more light on season 9's six-year time-jump via a flashback in episode 11, "Bounty." After The Walking Dead season 8 finale concluded the war with the Saviors, the first few episodes of season 9 finally wrapped up the story arc that began way back in season 6. Part of that was jumping forward a year-and-a-half in time. But after Rick's exit early in season 9, The Walking Dead dropped a bombshell and jumped forward another six years into the future.
In the episodes following The Walking Dead's six-year time-jump, it became clear that relations between Alexandria, Hilltop, and the Kingdom were strained. Plus, Oceanside's survival was unknown, while the Sanctuary had completely been dissolved - as Negan discovered following his escape from Alexandria. But the most interesting revelations were that Maggie left Hilltop to work with Georgie, Daryl was living on his own (apart from all the communities), and Alexandria suffered a tragedy that led to Daryl and Michonne's "X" scars. And now, some more clues as to what happened in that time-jump have been revealed.
At the beginning of The Walking Dead episode "Bounty", a flashback shows Tara and Jesus meeting with Ezekiel, Carol, and Jerry. In the scene, Tara gives Ezekiel a charter that Michonne had drafted prior to the time-jump; she took the charter from Alexandria because it was just collecting dust. As it turns out, the strenuous relationship between Alexandria and Hilltop - and, more specifically, Michonne and Maggie - began sometime early in the time-jump, before Maggie left Hilltop. This is based on Tara's comments about Alexandria not willing to do more for the Kingdom and Jerry revealing that he's having a child. Later in the episode, it's shown that Jerry's oldest child is about three years old. Plus, Carol's hair is still somewhat short in the flashback.
Even though all the communities came together to work on the bridge prior to Rick's exit in The Walking Dead season 9, it didn't take too long for them all to separate. While Ezekiel and Jesus continued to trade with each other, at least what was needed for both communities to survive (such as food and medicine), Alexandria pulled themselves out of the equation. Tara was apparently the only person willing to do more, and she ultimate left Alexandria for Hilltop, where she's remained ever since and may now even become their de facto leader following Jesus' death. Of course, Rick's decision to imprison Negan at Alexandria couldn't have been the only thing to drive a wedge between Michonne and Maggie, as they appeared to work out their issues in Lauren Cohan's final episode on The Walking Dead.
It's possible that whatever happened between them is linked to another season 9 mystery: the "X" scars on the backs of Michonne and Daryl. What Michonne went through is likely responsible for her attitude regarding letting new survivors join their community, as well as the formation of Alexandria's council, not to mention their strict rules. The Walking Dead's flashback reveals that this conflict also affected other characters aside from Michonne and Maggie. It clearly influenced Tara's decision to leave Alexandria permanently, which means that Tara must have sided with Maggie rather than Michonne. Hopefully, the remaining episodes in season 9 will reveal more about the event that so deeply divided Hilltop and Alexandria, as well as why they never reconciled.