It's been my long belief that we'd get a Knuckles-centered "Sonic Chronicles" adaptation! In fact I even came up with my own ideas for how it would go!
Focusing only on Knuckles, Tikal and Porker (maybe Chaotix as well), I had have it that:
1) Zachary is a member of the Nocturne Clan (A rival tribe of Pochamcamc); that survived the slaughter of the Drakon/ Echidna War by betraying their own kind to the Drakon Empire. They now live in an alternate realm known as the Twilight Cage (accessed only by a special portal ring, like the one that sent Knuckles to the Special Zone).
2) A small portion of Knuckles' Tribe survive as slaves of the Nocturnes (When I say small, I mean less than 50; the tribe is basically weak and few).
3) Among the tribe is "Nestor the Wise"; unlike his game counterpart, I'd have it the STC Nestor isn't a Nocturne traitor, but instead... KNUCKLES' UNCLE (how did he survive all these years? Like the game, the Twilight Cage would have mysterious space-time properties).
4) With the help of the Nocturne traitor Shade, Knuckles would save some of his tribe and return with them to the Floating Island.
From there anything could happen...
Of course, this is just my idea, where the story is gonna go is anyone's guess; I just hope, as well as you do, that we finally learn something about that creep Zachary, and the fate of Knuckles' people.