The cover for Knuckles: Endangered Species #1 (a.k.a. Sonic the Hedgehog Online #244) was based off of the cover art for both StH #211 and #245, as well as a promotional image for Sonic Chronicles: The Dark Brotherhood.
Trivia Tropes:
In Memoriam: StHO #249 was dedicated to the writer's father, who passed away two years prior to the issue's release.
Issue #250: Sally's de-roboticization, which was the route the original comic would have taken prior to Worlds Collide.
Schedule Slip: Apparently due to other side projects and numerous changes in management positions, some issues took longer to release than intended, at most a year. This allowed a reference to Sonic Universe Online #53 to be shown even before SUO #50 came out.
Putting into account when Knuckles: Endangered Species began as a separate project, it took a whole decade from the planning stages to being fully completed.
ASO was meant to be a comic version of Lost Hedgehog Tales, itself a What Could Have Been document for the Archie Sonic comic before the legal issues. This included starting at #237 (the first issue to show signs of the lawsuit), and having Hershey St. John be part of the Secret Freedom Fighters instead of Leeta and Lyco. However, since LHT went on indefinite hiatus and the staff wanted to make their own story anyway, ASO ignored the events of LHT, and began at #248 (with Hershey herself returning in #251).
Knuckles: Endangered Species initially began as an independent fan project, and had one completed page before being retooled. During this stage, without going into details, some Hostility on the Set led to one of the artists getting kicked out, only to be reinstated later when things calmed down, and then the project itself got retooled. That said, the writer had always said he was fine with an eventual ASO using this story as part of its storyline, so it was on the cards even before ASO became what it is today.
On that note, the writer was at one point trying to figure out ideas as to how to fit in the Krudzu, only to breathe a sigh of relief when Ian revealed the Krudzu wasn't part of the original plan for the published Endangered Species arc. The only remnant of the Krudzu in this version is an off-panel where he was used for a quick joke.
The team at ASO had plans for a remake of Chaotix Quest — in which Rob o' the Hedge and his family were written out of due to copyright issues and replaced with other characters. However, the team decided to leave Chaotix Quest as is, with plans to reveal what happened to Rob and his family to be given in the future. Granted, even back when it was only in the concept stage, one of the writers thought remaking the arc was pointless since the published story wasn't changed nearly to the same extent as Endangered Species was, meaning the story would've been mostly the same anyways. This in turn would've created unnecessary competition with the official work.
A story centering around Silver and Blaze was teased for Mobius Legends #4, but was not in the final release.
A Patreon account was planned for the comic at one point, but the plans were scrapped. Likely due to not wanting to run in legal trouble for trying to gain money off of what is essentially a fan project of an established series. note Considering how heavily protective Ken Penders is of his Sonic-made characters likely played a role in the decision as well.
Cubot's accent for #248 was intended to be a surfer dude's one. It was changed to a German one for the final product. The surfer dude accent later appeared in issue #250.
Plans for a Metal Silver was planned for #248, and it was even designed before it was cut out.
There was going to be more dialogue from the Secret Freedom Fighters in StHO #249, but they were either cut out or compressed. The only members who spoke in the issue were Elias, Shard and Harvey.
Amy was originally going to defeat Emerl by herself in StHO #249 instead of getting aided by Silver.
The Power Gem core embedded in Metal Sonic's chest from Sonic Universe #50 still exists—but it's within Metal Sonic's head rather than his chest.
Metal Sonic's override code for Mecha Sally, "SIGMA-THETA-MAKESONICSUFFER-ETA-OMIKRON-249", is actually "StHO 249 (Sonic the Hedgehog Online #249)"—in Greek. And with MAKESONICSUFFER thrown in, too.
