- For the unused concepts of other writers for Archie Sonic the Hedgehog, see Abandoned and Unused Concepts.
This page is dedicated to plot ideas and concepts conceived by or under head writer Ian Flynn that were never used in Archie Sonic the Hedgehog or Sonic Universe either due to the disapproval of SEGA or the legal issues surrounding Ken Penders' characters and concepts and the resulting reboot that followed Worlds Collide.
Ian had attempted to get E-123 Omega into the comic earlier than Sonic Universe #3. His first attempt would have him kill Tommy Turtle. His second attempt would have had him participate in the Destruction of Knothole. Sega nixed them both, probably because they didn't want a mainstream character caught in acts of mass murder.
Earlier plans for "Enerjak: Reborn" had it so that it was Constable Remington who would be the new Enerjak. This was abandoned when it was decided Remington was a not as familiar face to the readership, and that the arc would've spent too much time refreshing readers on who he is.
At one point, Ian considered showcasing the members of the Dragon Kingdom Freedom Fighters in a homage to the Furious Five from DreamWorks' Kung Fu Panda series. But the idea was ultimately scrapped, and the characters' identities remained a mystery.
Original plans for the story which began in Sonic #225 originally didn't include the "Genesis" saga. The first draft of the story, #225 would've ended with Sally's roboticization (an event that was instead moved to #230). It was decided by editor Paul Kaminski that what was planned wasn't enough to celebrate the Sonic franchise's 20th anniversary.
Sonic #237 was originally solicited as including a "mysterious figure" who would be following Sonic and the other members of Team Fighters. Though confirmed in the story to be Leeta and Lyco, Flynn later revealed that it was originally to be the MIA Hershey St. John. (1) Hershey was also intended to be included in the roster of the Secret Freedom Fighters but was replaced with Leeta and Lyco.
The original plans for the "Chaotix Quest" arc would've focused on Mighty and Ray's travels, while Espio sends word to the Shinobi Clan. Mighty and Ray would eventually find themselves encountering former Robians that were left deroboticized and without any homes; specifically Liza the Chameleon. Being unaware of the concept of robots, the Rainbow Valley chameleons forced her into exile out of fear upon being De-Roboticized. Feeling bad for her, Espio would've relocated her to his clan (explaining her cameo appearance during the "Iron Dominion" saga). Having been assigned to find and assist them, Liza would've followed Mighty and Ray, rather ineptly. Being somewhat uncomfortable around different people and not completely comfortable with her invisibility skills, her past life as an unwanted former Robian would've given her some common ground with Matilda and the others. 
During the actual Worlds Collide event, an early draft for the battle between the heroes and the team of Metal Sonic, Bass, and Treble included an idea for Metal Sonic and Bass fusing together in a fashion similar to the Super Adapter from the Mega Man series. The idea was rejected by either SEGA or Capcom but was referenced in the issue's Off-Panel. (2) This fused form of the two would have been vulnerable to Rouge Woman's Black Wave. (Source?)
"Lost Hedgehog Tales": Original Old Continuity Plans
Due to the effects of the Ken Penders vs. Archie Comics lawsuit, many elements of the comics lore had to be removed, rendering it impossible for the original continuity to move forward. As a result, Ian Flynn was forced to abandon his original long-term plans for the series, plans that reportedly stretched as far as the comics 300th issue. Before the effects of the lawsuit became apparent, it was known that certain planned stories had to be shifted to accommodate the inclusion of the Worlds Collide crossover storyline.
Currently, Flynn is in the process of compiling "Lost Hedgehog Tales", a completely independent work to let fans in on how his original long-term plans for the comic would've played out, as well as how the heavily edited "Endangered Species" storyline would've gone. The work is being split up into chapters, the first of which was released on October 30, 2015. On September 26, 2016, Flynn updated his post on Bumbleking, revealing that due to the current litigation regarding some of the affected characters, the project had been shelved for the time being.  However, on October 9, 2017, he stated that there could be a chance that the original continuity could be concluded in the IDW comics along with the new continuity. 
- The original storyline would have lasted 50 issues, from #225 to #275. The intent was to have the Freedom Fighters suffer a devastating loss that they couldn't easily bounce back from.
- Originally, #225 was planned to conclude with Sally's roboticization, before it was decided to create the "Genesis" saga in celebration of Sonic's 20th anniversary.
- Ian had, in fact, considered the possibility of Antoine D'Coolette dying after his sacrifice. After the overwhelming fan response to Sally's supposed death at the end of #225, as well as the reaction to Ant's actual sacrifice, it was unanimously decided to have him survive.
- An earlier draft of the "Loyalty" story arc (StH#237-#238), had Team Fighters encountering the previously presumed-to-be-dead Hershey St. John, whom had since gone undercover as a Dark Egg Legionairre. Hershey would have revealed that she never got the chance to let Geoffrey know that she was alive, but when told of his betrayal, she would have ended her duplicity and returned to New Mobotropolis.
- These changes came about primarily due to Sega's request that the "Olympic Trials" story in StH#242 be created:
- The "Heroes" story arc (StH#239-#240) was originally planned to be a three-parter: the first two parts would've focused on Team's Fighters and Freedom in their respective battles as normal. The third part, however (intended for #241) would've revolved around the newly-founded Secret Freedom Fighters and how they secretly helped to turn the tide for Team Freedom in their previous battle. In the end, the moments with the Secret Freedom Fighters were merely reworked and included in part two itself.
- Issue #241's "Unravelling" was first planned as a series of backup stories. Additionally, the story originally ended with Naugus merely tricking Geoffrey St. John. When it was decided that that wasn't a satisfying enough ending, the idea of Naugus possessing Geoffrey was made.
- Team Fighters battle against the Krudzu was initially intended as a story all to itself, sharing space with the "Olympic Trials" story in #242. When the latter ended up being longer than originally intended, however, the battle was reworked and shown in "Unravelling" instead.
All other information known by this point comes only from tidbits dropped by Ian and other creatives, including:
- The earliest draft of "Endangered Species" was planned as a Sonic Universe arc. Flynn intends to give a rough idea of how that version of the arc would've played out, as well as the original "unedited" edition of the main comic.
- Flynn stated that both versions had happier endings, unlike the version printed.
- Aleah Baker revealed that the arc would've marked the debut of a new design for Saffron Bee, of which she designed. She also stated that Saffron would've played a significant role in the arc.
- Shard and the Krudzu originally played no role in the arc.
- Bunnie Rabbot would've have been Legionized. Artist Tracey Yardley revealed on Flynn's blog several concept sketches for Bunnie showing off designs for her new robot limbs. Bunnie's silhouetted cameo at the end of SU#49 hinted towards this new design, it was revealed she was wearing a poncho to obscure her not-yet-finalized design. Several elements of her new organic body where later adapted for her design in the rebooted post-Super Genesis Wave timeline. 
- Dr. Finitevus would have been a "key player" in the lead-up to #275.
- According to Ben Bates, had it not been for the Worlds Collide crossover moving things around, #250 would've been the issue in which Sally was de-Roboticized.
Ian Flynn has revealed a number of details about ideas that were considered for the Worlds Unite crossover but rejected by Sega, namely:
- Including Phantasy Star Online as one of the Sega properties in the crossover.
- Having X join Super Mega Man and Super Sonic for the final battle with Sigma by undergoing a Super Transformation that would give him a gold version of his armor from Mega Man X4.
- Having Team Dark helping Knothole Freedom Fighters and the Unified Army.
Post-Shattered World Crisis
There were plans to continue the series following the events of the Shattered World Crisis, but the comic was eventually canceled due to SEGA severing their license with Archie Comics and switching to IDW Publishing. This change prevented these issues from ever being published.
However, the artwork for the comic interiors was later released online by their respective artists.
Metal Virus Saga
According to Ian, some of his unused ideas ultimately made their way into the IDW comics. Such is the case with the ongoing Metal Virus saga that was intended to occur after the 300th issue. Paul Kaminski introduced the original concept that led to the development of the Metal Virus saga to capitalize on the zombie craze of the early 2010s, but was shelved to avoid competition with Afterlife with Archie. The concept was later revived when Ian was recruited by IDW Publishing to head the new series.
Plans for the arc have been foreshadowed as far back as the Shattered World Crisis, with minor remarks of Dr. Eggman getting the roboticizer to operate again.
Aleah Baker's Contributions
- A deleted flashback in Spark of Life depicting Dr. Ellidy creating the AI that would become Nicole the Holo-Lynx. One of the prototype consoles would have resembled Nicole's early design from the television series' pilot episode.
- According to Aleah, Ian’s initial concept for Abyss the Squid was too birdlike. Other earlier designs had her being either more muscular and colored pink but she was told that villains could not be pink.
- The aquatic Mobians of Meropis were originally planned to have merpeople physiques before Paul Kaminski had it changed, saying they would be more versatile with regular humanoid bodies.
- One of Antoine's early redesigns for the new continuity had him wearing “form-fitting shorts”.
- Aleah goes into more detail on Clove and Cassia's backstory, revealing that the pronghorn sisters were orphans and were members of a nomadic society comparable to the Bedouins. Their mother would have been named Piper, and their father Sage. Piper was a councilwoman in this community until she died of ill health. When Cassia started to develop a similar illness, their father left to find help for a cure and never returned.
- When the truth about Cassia’s condition would have been revealed to her, Cassia would enter denial about her wellbeing and would have bitterly taken off on her own. She would eventually come into contact with a “compassionate force” (Aleah states it was a toss-up between the Freedom Fighters or G.U.N.) and get some development of her own while receiving treatment. Clove, meanwhile, would believe that her sister died out in the wilderness and lose all hope, only to learn the truth later during a Rotor-focused storyline.
- The relationships between Sally, Bunnie, Lupe, and Cassia would have been further explored. Sally's fondness for Nicole would also have been further fleshed-out.