The turbulent relationship between Sonic the Hedgehog and Shadow the Hedgehog is notorious in the gaming world, but the two super-powered rodents share a similarly chaotic albeit bizarre rivalry in the comics.
The game Sonic Adventure 2 introduced Shadow as a genetically engineered "Ultimate Lifeform" who wants the entire world to pay for the death of a girl who meant everything to him. As is his nature, Sonic inevitably gets caught up in this vengeful anger before helping Shadow see the light. Around the same time as Sonic Adventure 2's release, the now-discontinued Sonic comic book series by Archie Comics decided to take their shared history and blow it out of the water, giving way to a much stranger and confusing rivalry.
After covering the events of Sonic Adventure 2 in issue #98, the long-running comic book series brought Shadow back in Sonic the Hedgehog #146 during which time he's drawn to a lab that's emitting energy signals related to his original creator. There, he runs into Sonic who had come to investigate strange seismic activity in the area. It soon becomes abundantly clear that the headway they made during the events of Sonic Adventure 2 was all for naught, for a simple question from the Blue Blur fills Shadow with such unadulterated rage that the "Ultimate Lifeform" attacks him. Upon beating Sonic, Shadow decides to leave the unconscious hedgehog alive to continue his investigation, but he would later run into his blue nemesis at numerous intervals throughout their stay in the strange lab, during which time he would always resort to blows, spin dashes, and chokeholds.
During one of their many clashes, their conflict is so confusing that even Sonic can't help but ask why Shadow is acting so hostile towards him. Somehow, Shadow's response is even more baffling: "I sense you are my enemy--but I know not why." The utter ridiculousness of such a sentiment is, of course, impossible for Sonic to not call him out on, so Shadow comes up with a possibility: "Maybe I just don't like your attitude!" Although equally as bizarre, Shadow would later fight against Sonic for a more understandable, acceptable reason: He finds out his creator is Dr. Eggman's grandfather, so why not join forces with him? So he does in issue #160.
Originally, the main source of confusion regarding Shadow's animosity towards Sonic could be traced back to Archie Comics' decision to tie in the events of Sonic Adventure 2 with the comics. It could have worked if the series had not proceeded to wipe away the supposed friendship they formed during that game by making Shadow suddenly hate Sonic for no apparent reason. It's even more baffling when considering that Shadow learns much later in issue #171 that he had been created to protect the planet Mobius, which is also Sonic's purpose. So this "sense" Shadow felt cannot be blamed on his programming.
Of course, it's understandable why the comics decided to go this particular route. Making Sonic and Shadow enemies is far more entertaining than Shadow just being a loner, as he is portrayed in IDW Publishing's rendition. Ironically, the series initially gave Sonic and Shadow a logical reason to fight each other immediately following the Sonic Adventure 2 tie-in issue. In issue #124, Shadow falls from space and lands unconscious on the planet's surface before proceeding to punch Sonic accidentally upon waking up, causing Sonic to fight back. Of course, their conflict would immediately be put on hold, as Mobius had just fallen under attack by the alien race known as the Xorda. Regardless, it would have made much more sense if Sonic the Hedgehog and Shadow resumed their fight after the alien conflict had been resolved and based it all on this common misunderstanding. Alas, this didn't happen.