However, things soon became clear that Penders might have that leg and Archie, in a panic, made a number of changes to the comic. 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. Penders countersued and the two went to court. Archie sued Penders under the idea that anything and everything created for the comic was now Sega's, not his. 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. Penders has said three conflicting accounts as to what happened - either there was no contract, an intern destroyed his old contract or a fire destroyed his contract. 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. In issue #160, Flynn took over, streamlining the comic from its glut of characters and out of control love triangles. 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. 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. In anger, Bollers quit the title and Penders took back his old title as head writer. When Penders' work with Knuckles came to an end, both writers would find themselves working together, leading to the two butting heads. 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. 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 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.

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