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Be warned there are Walking Dead comic spoilers below that may tie into how the TV show handles things.
To say that The Walking Dead is changing things up in Season 9 is to say that walker guts smell kind of gross. The narrative is making a big time jump (or two), a bunch of new characters are getting introduced, and it's Andrew Lincoln last season as Rick Grimes. It will also be Lauren Cohan's last episodes as Maggie Rhee for the foreseeable future, with the actress starring in the new ABC dramedy Whiskey Cavalier. Cohan revealed recently that Maggie's exit will be open-ended, and looking back to the comic book source material may clue viewers in on how that exit will be handled.
Why Would Maggie Even Leave?
When The Walking Dead Season 8 came to a close, the finale gave fans the hint of deep-seated turmoil coming to the protagonist communities, with Maggie and Daryl furious that Rick allowed Negan to live, rather than giving the Saviors leader the big death he arguably deserved. The first Season 9 trailer showed off Negan's new jail cell digs, but viewers shouldn't expect Maggie to soon be overjoyed and gracious for Rick's return to old-world authority and punishment. Every second that Negan stays alive is another reminder of how he brutally took Glenn's life.
And because no one can keep a charismatic villain like Negan locked up for good, it should surprise no one that Negan ends up getting free at one point or another. The first time, his cell is accidentally left unlocked, but the villain chooses to stick around to prove his redemption and rehabilitation to Rick. Later, when another escape scenario is put forth by someone else within the community -- I'm hoping the TV series makes it a more important character than the one used in the comic -- Negan takes advantage and goes on a very interesting journey that doesn't really need to get discussed here, as to not spoil other plotlines.
Yadda, yadda, yadda, things happen and Maggie finds out that Negan is free, which does not hit very high on her list of comforting and enjoyable discoveries. And so, when the time is right for it, Maggie strikes out to follow the expletive-spewing villain, which gives the character her own interesting journey of self-discovery. There's no doubt the live-action adaptation will change some things up on this front, especially since Maggie isn't meant to return for TV soon.
Where Could Maggie Go?
As stated earlier, it's assumed that Maggie will be taking off as a way of tracking Negan down after he takes his own leave of absence from Alexandria's walls. In the comics, Maggie's trek doesn't appear to take all that long, with seemingly less than a day's travel on either end of the trip. So for the character to potentially remain free and clear of Hilltop for the remainder of Season 9, it's presumed the TV show will greatly expand on how her Negan hunt goes down. And it's likely that will happen after Alpha and the Whisperers' introduction (which apparently won't crossover with Rick's remaining time).
Without going into spoilers about how Maggie's journey plays out, I can say that I'm not immediately sure how The Walking Dead will suitably justify keeping her away from the rest of the group. If the show follows the comics generally enough, it's possible that Maggie will eventually come to the realization that getting revenge on Negan will do nothing to bring Glenn or her all-around happiness back, which could extrapolate into her believing that there is nothing left for her to return to back at Hilltop and the other communities.
As such, Maggie might follow in Morgan's footsteps by striking out on her own, either with the intention to stay alone or to find a new group that doesn't remind her of all her past tragedies. But that would create the complication of either having to leave her baby behind with others, or taking the toddler with her, with the latter option highly unlikely to happen. In the comics, this is also a point when Maggie actually enters into a new romantic partnership, though I also can't see the TV show diving into that. So until we learn a little more, the comics might actually be more of a guideline to show us what probably won't happen to set up Maggie's final episodes.