Cash Cow Franchise: For almost two decades, the Sonic comics were Archie's highest selling series.
Creative Differences: Penders vs. Bollers got so bad, it ended with them both leaving the comic simultaneously. According to Penders, the editor of the comic forced him to bail because he kept on changing his stories, the final straw being the Mobius: 25 Years Later story. More specifically, he stated that there would be no more work done on said story until Penders included other characters from the games, such as Shadow. Penders quit in response.
Ken Penders only official remark on Ian Flynn's tenure as writer was in an interview where he basically called Flynn a hack who was just using story ideas he came up with before he left Archie, even though he admitted that he refused to actually read any of his stories, and swore to dismiss all of Flynn's issues as Canon Discontinuity if he was ever head writer again. In response, Flynn's only official remark on Penders was to rebuff his predecessor's claims and establish that all his stories were his original ideas.
Per word of Aaron Webber, Archie in general seems to pretend that their Sonic comics never existed once they lost the license, due in part to them and Sega apparently departing on sour terms and Archie wanting to move on from the series anyway.
Several writers have admitted that Princess Sally Acorn is their favorite character.
In one Q&A, Ian Flynn described Guru Emu as his favorite Downunda Freedom Fighter to write, given that his peace-loving, mystic ways are such a departure from the other members of the group.
End of an Age: The comic was the last remnant of the American version of the Sonic franchise that was featured throughout the 1990s.
Executive Meddling: The series had a lot of issues of Archie suffering this under Sega. To date, here is a known list of all the official mandates Sega has imposed on the comics, along with other baggage they've brought into the comics.
Certain characters, including certain ones from the games, are off limits for use, such as Eggman Nega (who is not only barred from unobstructed appearances, but can't even be fully named on-panel) Mephiles the Dark and Black Doom (although the latter is still allowed to cameo in flashbacks and the Black Arms race is free for use) due to being dead. It also took years for characters like Cream the Rabbit and her mother to be allowed to appear in the comic, same with Emerl and Omega. Certain characters like Blaze the Cat and Marine the Raccoon had so many restrictions with what could or couldn't be done with them that the most they could do was just make cameo appearances.
Game characters can not have parents or relatives. This also caused the Continuity Reboot to change things up, such as the fact that Uncle Chuck isn't blood related to Sonic anymore, and that the title is honorary.
Sonic cannot get overly emotional (which is often paraphrased or misinterpreted as "Sonic can't cry.").
The name "Mobius" cannot be spoken or mentioned as the name of the planet, and it is not allowed to be called "Earth" either—Sega says it is now just "Sonic's World".note They still call themselves "Mobians" though.
Originally, the SEGA cast couldn't be implied to have aged to the point where they are now or age further. The Classic forms of characters couldn't be implied to be younger forms of the characters either. This mandate has been officially lifted as of the comics reboot, as the Sonic Mega Drive comic uses the Classic designs as the characters younger counterparts (and not long before that, a post-reboot issue featured a flashback to the proto-Silver Sonic that used Sonic's classic design).
Characters originating from Sonic Underground, the OVA, and Sonic X cannot make an appearance. According to a Q&A by Ian Flynn, this is due to Sega not being keen on giving attention to any past incarnations of the franchise. As such, they forbid the use of any character from the aforementioned pieces of media.
Part of why Knuckles and the echidna race had so much build-up back in the day is that Sega vetoed ideas that were originally meant for Sonic, yet went through with no problem when applied to Knuckles.
As of the reboot, every non-Sega, SatAM, AoStH, and Ian Flynn character has been removed until further notice. While he hints that he can use Sonic Underground, he didn't use characters like Manic and Sonia without their in-series background of being Sonic's siblings in the end, mostly because he knows the Underground fandom would get up in arms.
Ian originally wanted the arc leading up to Issue 250 to be about the Freedom Fighters rescuing Sally with her being de-roboticized in the milestone issue. However, due to the Worlds Collide crossover, these plans were aborted and Sally was returned to normal thanks to the reboot.
Ken Penders himself attempted this trope. After winning the lawsuit, he remarked that he would be willing to allow Archie to continue using his characters as long as he received royalties for every issue they were used and he had creative control over how they were used. However, both SEGA and Archie had no intention of ever working with him again and the comic rebooted and removed all of the characters and concepts he introduced.
All of the 170+ characters created by writer Ken Penders have been permanently removed from the series due to a major lawsuit with him, including several major characters and series mainstays. This also included characters created by other writers pre-issue 160 like Karl Bollers as SEGA didn't want to risk anything similar to the Ken Penders legal case happening again in the future. In some cases, even unrelated characters of writers still at Archie (like Angelo Decesare's characters) got removed.
While Eggman Nega technically does exist in the Archie series, he is not allowed to make an unobstructed appearance or even be fully named (only being referred to as "Doctor Nega") because of unexplained hangups with Sega. Also affected by unusual hangups are Tiara Boobowski and her father Gazebo, from the canceled game Sonic Xtreme.
Black Doom and Mephiles are off-limits for similarly unexplained reasons (though it could be because they are both dead in canon). The former caused Ian Flynn to create Black Death.
Tundra's true identity was guessed by quite a few people.
Once the the comics hit a delay at the start of 2017, many called that the comics were likely cancelled. On July 2017, that was indeed confirmed.
When Sega announced that the comic was seeking a new publisher, many guessed that IDW Publishing was be a likely candidate due to having hosted many a property (Hasbro, many Cartoon Network series, etc). Sure enough, Sega announced that they had signed a deal with them. 2 days after their announcement of the canceled Archie comic.
The Sonic/Image crossover is at best unlikely to be reprinted, and so is the first story in Sonic Live.
With Archie losing the Sonic license outright, the entire series became this, as Archie lost the rights to reprint or sell issues or volume collections of the comic. The only way the series will ever will be if IDW, the new license holder of the comic, decides to reprint the comic. While IDW is known for re-releasing or even reviving old comic book series, it's doubtful that they or SEGA would want to risk possibly continuing the all the legal problems of the comic.
Ken Penders apparently gained some reprinting rights in his settlement with SEGA and Archie, as he intends to digitally release the "Mobius: 25 Year Later" stories alongside The Lara-Su Chronicles. However, the comics are likely to be heavily edited in order to avoid further legal issues with SEGA.
While the comic was abruptly ended at Issue 290, the comic had solicits promoting Issues 291 to 294. Likewise, Sonic Universe ended at Issue 94 but was solicited through Issue 97. The pencil art for a few issues have been released and it's likely that at least one or two of them were fully completed before SEGA took the Sonic license from Archie.
Tyson Hesse confirmed that Sonic Mega Drive's third and final issue was completed before it was canceled and he hopes that one day it will get released.
Archie had advertised a Sonic comic for Free Comic Book Day. It would have depicted the first fight between Sonic and Dr. Eggman in the post-reboot universe. Due the comic's cancellation, it was quickly swapped out with a Riverdale comic.
Throughout the late 2000s and early 2010s, Ian Flynn ran a blog on Archie's website where he answered fan mail as both himself and as characters from the comic. It also hosted a prose style prequel and epilogue to the "Dark Mobius" story line. Due to the website getting redesigned, the blog and all its entries were deleted.
Name's the Same: Black Death, the Black Arms alien from the new continuity, shares the same name as a one-off Mobian villain from the previous continuity.
No Export for You: Due to the legal mumbo-jumbo the whole comic has suffered along the years, not to mention the lack of popularity of the video games outside animated adaptations in that region, the comics aren't translated in Latin America.
For a long time, it was impossible to find the series in the United Kingdom as well, because the license didn't cover the territory. Instead, Fleetway used to produce Sonic the Comic.
Old Shame: Though not the writer on the story, Jonathan "WB" Gray, one of many a Promoted Fanboy, absolutely regrets being the guy who drew "The Slap." He has expressed similar resentment towards the "Sonic's Angels" story, a story which infamously depicts what can only be described as borderline Torture Porn being performed on poor Bunnie.
Print Long-Runners: The longest-running comic book based on a licensed property, video game or otherwise, ran from November 1992 to July 2017; 24 years.
Post-Script Season: The comic effectively was in this state after the "Endgame" arc in issues 47-50, with Sonic emerging victoriously after a climatic battle with Dr. Robotnik, resulting in the death of the latter. This was supposed to be the Grand Finale of the comic, as the writers at the time expected that it would soon be cancelled, but due to great sales numbers, the cancellation order never came down upon on the comic, and it continued onwards. How long exactly the comic was in this state is the subject of some debate; some would say that the return of Dr. Robotnik (or rather Robo-Robotnik) in issue 72 in preparation for the comic adaptation of the Sonic Adventure was were this stopped being the case, while others are of the opinion that this first truly happened when Ian Flynn took over as headwriter with issue 160 and effectively ended the Dork Age many readers felt the comic had been languishing in for years at that point.
Promoted Fanboy: Several examples, most prominently current head writer Ian Flynn who was known as the author of a popular fan comic Other-M. He originally was became known to Archie Comics by sending unsolicited story proposals, but when Ken Penders abruptly quit he was offered the position of head writer, meaning he went from being a fanboy to having creative control over his favorite comic overnight. Since then, he has gone on to become one of the better known names in gaming comics, regularly being hired by both SEGA and Nintendo to make comic adaptations of their games.
Recursive Adaptation: The comic had already started to incorporate some plot elements from Sonic Chronicles, which itself had seemingly borrowed and modified some of its echidna lore material from the comic.
Role-Ending Misdemeanor: After the lawsuit by Ken Penders, his demands for creative control and royatlies on any material that used his characters, along with several accounts of unprofessional behavior, it's likely that no publisher will ever let him write a comic book for them again.
The trade paperbacks. Most recent ones have been pushed back at least once, and some have been outright cancelled. The last one came out in April. Read more in this (very long) thread.
Between late 2015 and early 2016, issues of the main series and Sonic Universe were taken off of their original release dates and postponed for undisclosed reasons.
Early 2017 likewise saw a slip in the schedule of both series as well as the "Mega Drive" mini series.
With Archie losing the comic license and being given to IDW, it's unlikely any stories that were caught in this will ever get out of it.
Screwed by the Lawyers: The ongoing lawsuit by Ken Penders led to the vast majority of the cast up and disappearing. As of #252, the entire universe rebooted, with 256 establishing that the whole multiverse implodes on itself and was rebuilt. The new universe gradually but completely overwrote the old, including memories, so the old world was completely gone.
While SEGA had always been prone to put restrictions on what the comic could and couldn't do, the chaos surrounding Penders' lawsuit caused them to take a much more active role in managing the comic and they issued many story mandates after the comic rebooted.
These legal problems came to a head in July 2017, when SEGA just up and cancelled the comic outright.
Shrug of God: When asked about the fate of Robotnik's parents, Flynn posted two ideas. One was that Robotnik "did away" with them. The other was that they migrated to the United Federation. In either case, the writer leaves it up to the reader.
Torch the Franchise and Run: In his final "Mobius: 25 Years Later" story line, Ken Penders had the entire time space continuum collapse in on itself, with only Sonic and Lara-Su surviving so he could potentially continue the story later on. However, when Ian Flynn began work on the comic, he decided to give the story a soft reboot as "Mobius: 30 Years Later" and he also created an alternate version of the story in his "Dark Mobius" story line. However, due to Penders' lawsuit, Archie lost the rights to his stories and characters and Penders is now planning to create his own continuation of the story.
Troubled Production: The comic always had a problem when it came to converting video game storylines into its largely different setting. However, two of the biggest screw ups came about via Sonic Adventure and Sonic Adventure 2. For Sonic Adventure, Sega gave Archie a copy of the game... untranslated, so they had to fudge a lot of the story. The original plan was to have the storyline run through then-all three titles - Sonic the Hedgehog, Knuckles the Echidna and Sonic Super Special. However, just before the storyline started, the Knuckles comic got cancelled, forcing Archie to cram all of the Knuckles stories into the Sonic issues as back stories.
For Sonic Adventure 2's story, the big problem was that Sega was insistent on Archie creating a tie-in into the game. Archie's solution? Just do enough to whet people's appetite and go get the game. Still was enough to ruin a side-by-side storyline that had a cosmically-powered Knuckles altering Mobius drastically.
From Sonic Adventure 2 onwards, most adaptation storylines ended up just usually being short teasers following the issues main story. The teaser game stories have boxes that clarify whether the game in question is to be taken as canon in the comic's universe or not.
And then, there was the problem with Ken Penders and Karl Bollers. Around 1997-98, Karl Bollers took over the Sonic comic as Penders focused on the Knuckles comic. However, Ken would end up shuffling back over to Sonic due to the Knuckles comic getting cancelled. At first, things weren't too bad, as Penders could focus on the Knuckles back up stories. However, come #125, those were done away with and the two were working together. Suddenly, the two men were trying to pull rank over one another over story elements and which way they wanted the story to go. Ultimately, Bollers quit while Penders stayed on for a few issues longer before being let go, with newcomer Ian Flynn being asked to go from simple one-story back up writer to Head Writer. A few years down the line, Penders decided to reclaim his characters and storylines, copyrighting them all with Archie and Sega being notified of this. Archie sued Penders, claiming that the characters he created were Sega's, Penders counter-sued and we're off to the races.
In the end, both sides kept shooting themselves in the foot and, ultimately, they settled, going so far as to have Archie utterly reboot the series from the ground up.
On the subject of Sonic-related works connected to Ken Penders, there's the exhausting story concerning what became The Lara-Su Chronicles. The original story was initially called "Knuckles: 20 Years Later" and was meant to be an issue of Sonic Super Special. However, SSS got cancelled with issue 15. The story was refined and rebranded as "Mobius: 25 Years Later", serving as back-up stories in the main title. However, Penders left the story on a cliffhanger and soon quit Archie due to Executive Meddling (they wanted him to add more Sonic characters to it). He regained usage of the characters thanks to the lawsuit and promised to tell the tale he wanted to with a release date of July 2015. As of this writing, it hasn't been released with the excuse of "wanting to translate it to other languages" being the reason.
The problems for Archie wouldn't end with the reboot. Mega Man's title was flagging sales again and Archie decided it was time for a second crossover. Enter Sonic the Hedgehog/Mega Man: Worlds Unite and Archie decided to make it bigger - not only did they involve both main titles along with Sonic Boom (though relegated to just Sticks the Badger, Fastidious Beaver and Comedy Chimp) and the main heroes of the Mega Man X series, but a dozen other franchises from SEGA and Capcom, which cost Archie millions in licensing costs. Unlike Worlds Collide, Worlds Unite was a mixed bag and given a lukewarm reception with Archie barely recouping the costs. This lead to Sonic Boom and Mega Man to be shuttered afterwards as a cost-cutting measure (Though Boom was more due to the backlash from Rise of Lyric's failure.) and the Sonic titles were hit hard as the crossover smashed into the ongoing Shattered World storyarc. The title would go into a brief hiatus soon after, a result of Archie rebooting their entire main line and go on a second, much longer hiatus that would lead to the title's cancellation and the license being sent to IDW Publishing. The exact reasoning for Archie losing the license isn't known, but hints from various sources seem to hint that the Archie reboot drained them financially and their focus on Riverdale lead to Archie to be very lax on the idea of keeping the series despite it being one of their best-sellers.
The original plot for "Endgame" really did involve Sally's demise — her apparent restoration later on was to have been a robot double, the truth only slowly coming out later as "Sally" began to act increasingly suspicious and out-of-character.
Ken's stated that some of the original ideas for the Princess Sally miniseries included a roboticized Queen Alicia ruling over her own subjects as a threat to both the Freedom Fighters and Robotnik. Another was a Thelma & Louise type story with Sally and Bunnie. Sega vetoed both of these ideas, wanting to use only Sally and Robotnik. This is what led to the Substitute Freedom Fighters and Geoffrey St. John. Regarding the Source of All, one of the ideas that Ken was brainstorming with a friend of his was that the Source was actually an AI made out of a pool of nanotechnology, from either the past or the future, that was so advanced as to be indistinguishable from magic. However, they never figured out what its motives were before it was nuked.
Both Karl Bollers and Ken Penders have made public their plans for the comic had their employment at Archie continued.
When Ian Flynn took over as main writer, he decided to write out a couple of Penders and Bollers' lingering plot points, leading to some cases of Fauxshadowing.
Robotnik at one point had problems with an unseen person who called themselves "Anonymous", showed themselves very adapt at reprogramming robots and computers, and Robotnik noticed that "Anonymous" from all evidence appeared to about as tall as himself. The idea was that this "Anonymous" would later be revealed to be Robotnik Prime, who was Back from the Dead for real this time. Instead, it was revealed it was actually A.D.A.M. who was behind it all.
The end of "The Good, the Bad, and the Unknown" arc was very heavily setting up that Ivan Kintobo, an ancestor of Robotnik and creator of Shadow, had survived as a Human Popsicle and implied that he was going to be a major antagonist. The comic would later reveal that Ivan was actually long dead as he had not survived being frozen down.
Ian Flynn originally intended to have E-123 Omega off Tommy Turtle, but Executive Meddling had that changed to the Egg Fleet. In fact, Executive Meddling kept Omega from appearing in the comic for some time since Karl Bollers tried to put him in. It wasn't until issue 3 of Sonic Universe that he made an appearance.
One of the biggest cases of this was the Endangered Species arc. Part one had font that was obviously put in at the last minute to keep from referring to certain characters by name, while the rest was completely rewritten to remove them altogether. The arc was controversial at best as a result.
Flynn has also gone on record to say that the early implied romance between Tails and Barby Koala (of the Downunda Freedom Fighters) is "completely one-sided and kind of creepy", (most likely due to the age difference, with Tails being around 11-12 and Barby appearing to be in her late teens) and that as long as he's on the comic it's not going to happen.
Ian Flynn was writing an essay known as the "Lost Hedgehog Tales," which would explain his original plan for the series, before the Ken Penders lawsuit, leading up to issue 300. He released one chapter but due to possible legal issues, as well as the possibility that he might utilize the unused plots for the IDW comic, he has put an indefinite hold on releasing any more.
Chapter 1: Antoine was originally going to eventually die to Metal Sonic's explosion, but was saved by the fan reaction to his injuries. Also, Hershey the Cat wasn't dead after all.
Ian Flynn really wanted to write a conclusion to Sonic Underground, but Executive Meddling always got in his way. He came close to being able to release the story in the fiftieth issue of Sonic Universe, with official promo art even being released, but those plans were nixed in favor of writing a lead up story to Worlds Collide. And thanks to the Cosmic Retcon destroying the series' multiverse, the chances of the story ever being released are unlikely.
Cortez and Null were two villains planned for Sonic Universe issues that never were made due to the cancellation.
Ken Penders has recently said that his plans leading to Issue 200 would have been the "Mobius: X Year Later" timeline and the main comic's timeline being disrupted and the comic would have rebooted with Issue 200. This conflicts with his other claims that he intended Issue 200 to depict Antoine and Bunnie's wedding.
Ken Penders got around the CCA somehow by hinting at one of the characters in the "Mobius: X Years Later" storyline being gay... and somehow doing this while showing the life partner, threading the relationship into the text. Once fans started searching, it became obvious (and confirmed by Ken), that the hinted couple was Rotor and Cobar, the latter an echidna scientist from the Dark Legion.
In the new continuity, Gold the Tenrec was confirmed to be either bisexual or lesbian (her creator hadn't decided yet).
Current writer Ian Flynn has organized his own message board, where he and other creators interact with fans and answer their questions. His predecessor, Ken Penders, also kept up a message board while he was writing for the comic, which is still active and occasionally talks about the stories that he had planned for the series.
The events of Sonic the Hedgehog (2006) occurred in the comic as they did in the game, including the Cosmic Retcon. Soleanna has been mentioned a few times and issue #246 has a brief appearance of White Acropolis. The Complete Sonic Comic Encyclopedia describes it in more detail, including entries on Iblis, Mephiles, and Solaris.