Fear The Walking Dead's mid-season premiere addresses Morgan Jones' departure from the main show, and also hints why he's not going back. Played by Lennie James, Morgan Jones is a veteran of the zombie apocalypse - the first man Rick Grimes meets after awaking from a coma and realizing the world had taken a hard left during his absence. Morgan finally joined up with the main Walking Dead cast in season 6, arriving in Alexandria just in time to see a blood-covered Rick execute another resident. But throughout his time on the main show, Morgan could never quite decide whether to be an uber-violent warrior or a zen pacifist, and eventually walked away without saying goodbye.
Obviously, Morgan's exit from The Walking Dead was designed to facilitate his arrival in Fear The Walking Dead, but from an in-universe perspective, his long walk across the U.S.A. has remained a bit ambiguous in terms of what he hoped to achieve. Also strange is why Morgan has abandoned efforts to return to Alexandria - especially now he has a hat, an axe, and a new attitude. Once Ginny is dealt with, Morgan would have the perfect opportunity to go home, but is building a new community instead. Although we know the real reason (Lennie James is far better served in the spin-off), the canon explanation isn't so clear.
Morgan rarely talks about Rick and the old gang in Fear The Walking Dead, but season 6's "The Door," gives the most detailed insight yet into why Morgan left Alexandria - and also why he isn't heading back there any time soon. "The Door" finds John Dorie in much the same headspace as Morgan was toward the end of All Out War. John believes that his conflicted attitude towards killing has corrupted his soul, and endangered those around him. To solve this imaginary problem, Garret Dillahunt's John isolates himself and contemplates suicide. Talking sense into the sharpshooter, Morgan refers to his own experiences, imploring, "you're like that guy who walked halfway across the country to get away from the people he cared about most and found himself sitting across your campfire."
When he first switched shows, Morgan would often say "I lose people, I lose myself" - a fairly meaningless TV soundbite. By comparing Morgan's departure to John's current dilemma, however, Fear The Walking Dead gives a far more substantive idea of why Morgan left Rick behind. Morgan couldn't live with the body count necessary to protect his friends against people like the Saviors, but also couldn't live with the guilt when his mercy resulted in the deaths of allies (which is exactly what happened with the Wolves). Morgan didn't leave Alexandria to escape the people he knew; it was a misguided self-imposed exile designed to "protect" those he cared about, while punishing himself. Had Morgan Jones owned a remote cabin like John Dorie, he probably would've gone there instead and saved himself the legwork.
More interesting is how apparent Morgan's regret is - how deeply he wishes he hadn't turned his back on Rick and the others. Despite this, Morgan strongly suggests that he has no longer has any intention of returning. Continuing his speech to John, Morgan explains that Fear The Walking Dead's survivors are his "family" and sole focus. Morgan considers meeting John, Alicia, Daniel, not you Strand, Dwight, and the rest as some kind of divine providence, and rather than traveling to Alexandria as previously planned, he's now determined to create a community with his new family from scratch. Morgan even calls John his "best friend." Thankfully, Rick Grimes wasn't around to hear that one. Whereas Morgan once sought to take his new pals to Alexandria, it seems the Ginny ordeal has strengthened their bond, effectively overtaking Rick and co. as the people Morgan feels closest to, leaving him with no reason to return. No doubt meeting Grace is another big factor in Morgan's change of heart.
As he explains his reasons for running away, there's a detectable hint of shame in Morgan's voice - a deep remorse that he still carries in Fear The Walking Dead season 6. Deep down, Morgan perhaps doesn't want to face Rick, Carol, Maggie, and the others, explain why he abandoned them, and then humbly request his people be taken in. It's almost as if Morgan can guess all the ordeals Alexandria suffered in his absence (Rick's disappearance, Whisperers, etc.), and how desperately they could've used his help.