- 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 had 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 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 back-up 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 for 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.