Archie Comics' Sonic The Hedgehog "Endangered Species" (Lost Original Storyline; 2013)
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History and the Lawsuit
In 1994, writer/artist Ken Penders joined the comic with issue #11 and stayed on until 2006 with issue #159, spending some time away to work on the spin-off comic featuring Sonic's friendly rival Knuckles the Echidna. During this time, Penders helped create a number of characters, locations and lore that expanded on the sparse backgrounds for many of the characters, though greatly went overboard on Knuckles' backstory. In 2000, the Knuckles comic was cancelled and the stories he planned were absorbed into the main comic, leading him to work alongside writer Karl Bollers. When Penders' work with Knuckles came to an end, both writers would find themselves working together, leading to the two butting heads. In anger, Bollers quit the title and Penders took back his old title as head writer. However, after assumed executive meddling from his bosses concerning what he felt was his biggest work "Mobius: 25 Years Later", Penders would be released from the title. To quickly keep the title afloat, Archie asked up and coming writer Ian Flynn, known in the Sonic fan community for the fan comic "Other-M", to take over for the departed writers. In issue #160, Flynn took over, streamlining the comic from its glut of characters and out of control love triangles.
In 2009, Penders sought to obtain his old contracts from Archie, only to learn that the contracts they had were oddly done - they referred to his work, but nothing about the characters he created. Penders has said three conflicting accounts as to what happened - either there was no contract, a clumsy intern destroyed his old contract or a fire destroyed his contract. Thus, wanting to regain control of his characters as well as gain payment for reprints using his work, Penders copyrighted his characters, then sent a notice of copyright to Archie Comics. Archie sued Penders under the idea that anything and everything created for the comic was now SEGA's, not his. Penders countersued and the two went to court. Until 2012, Ian Flynn, the crew of the comic and the fans were under the assumption that Penders had no leg to stand on and that the comic would be safe. However, things soon became clear that Penders might have that leg and Archie, in a panic, made a number of changes to the comic. In 2013, in the aftermath of the crossover storyline Sonic the Hedgehog/Mega Man: Worlds Collide, the comic underwent a major reboot which jettisoned all characters and concepts not created by SEGA or Ian Flynn
At the time of the lawsuit, the comic was going through a major storyline where Sonic and his friends were on a globetrotting quest to rescue Princess Sally Acorn from Dr. Eggman, who was using his as the robotic Mecha Sally. Issue #243 kicked off the storyline "Endangered Species", which saw Sonic stopping in the Echidna colony of Albion, aided by Knuckles as they sought to protect the last of the Echidnas from the Dark Egg Legion, Eggman's soldiers, and Thrash the Devil, the last Tasmanian Devil who sought to punish the Echidnas for the eradication of his species. Issue #243 ended with Sonic in battle with the Dark Egg Legion's leader, Lien-Da. When Issue #244 started, everyone save Sonic, Miles "Tails" Prower and Amy Rose was gone. It was later revealed that issue that an incident involving the colony's security defenses knocked everyone out and Thrash, finding everyone, set Sonic, Tails and Amy aside and launched every last echidna through a warp ring into another dimension. The last two issues saw an enraged Knuckles battle Thrash while Sonic and his friends dealt with a modified Metal Knuckles.
According to Ian Flynn, the story was never planned to be that way. In fact, it was supposed to have a happy ending. While Flynn is currently writing up a document that would tell more of this story and more of what Flynn had planned had the comic not been rebooted, already a few things had been discovered by fans. The first was a set of original print drawings by Issue #243's artist Steven Butler [which showed off some of the unaltered text], the first signs of alteration. The second was the cover to #244. The original cover had a smaller profile shot of Amy Rose standing back to back with Knuckles' comic-established love interest Julie-Su. The cover to #245 was originally mean to have Lien-Da ensnaring Sonic with a metallic whip. A second cover removed Lien-Da but kept the whip and the final cover added leaves to the coiling, marking the change from using the Dark Egg Legion to just the cybernetic plantlife Krudzu. According to Flynn's wife, the storyline would had also involved Saffron the Bee, the comic-established fiancee of Chaotix character Charmy Bee, who would have obtained a new look.
Currently, it is unknown how much of the original story was worked on before the forced changes and if they exist in some way outside of what is available now.