A scene from the opening credits of Rick and Morty may hint at the real origin of Evil Morty. This version of Morty from an alternate dimension has been an antagonist since season 1. Despite how long he’s been around, Evil Morty’s only appeared a couple of times, neither of which has put him directly up against the main protagonists, C-137 Rick and Morty; instead, Evil Morty acts as an antagonist to the Citadel of Ricks. The mystery behind Evil Morty's origins has never been explored before; however, a moment in Rick and Morty's open credits may reveal why this character hates all Ricks.
Evil Morty is like a number of other characters, such as Phoenixperson, Zeep Xanflorp, and Supernova, who are out there biding their time before they come into conflict with the main Rick and Morty again. Evil Morty is particularly intriguing, being the only version of Morty who got the upper hand over a version of Rick, making him a potentially significant antagonist. Despite the setup, viewers have no idea where he really came from yet.
A theory presented by similar to the Cthulhu scene. The scene has Rick and Morty running away from some unidentified monsters. Rick uses his portal gun to escape, but the portal closes before Morty can get through, leaving him to be attacked by the monsters.
There’s no direct evidence that this is his origin, but it’s a strong explanation for why Evil Morty is the way he is. This Morty managed to fight off the monsters on his own, without needing Rick. His Rick may have returned or not, but even if Rick returned, this Morty wouldn’t have welcomed him. Why would he need the old man who saw him as disposable and left him behind to be attacked by monsters? This is suggested when Evil Rick, under Evil Morty’s control, taunts Rick C-137, saying that Ricks don’t care about Mortys, backed up by the Morty Torture Chamber appearing in the same episode. If this is what Evil Morty believes (and some Ricks seem to agree with it), then it makes sense he was horribly treated by his Rick, perhaps even being completely abandoned, a feeling that got more twisted over time.
The Rick and Morty theory explains why Evil Morty’s grudge and villainy go so deep. He hijacked his Rick’s brain to kill 27 other Ricks and enslave a bunch of Mortys in “Close Rick-Counters of the Rick Kind.” When he reappears in “Tales from the Citadel”, he gets elected as President of the Citadel, then kills everyone who opposed him, effectively becoming a dictator. This is no minor grudge, and being abandoned by his Rick would fuel that. He’s taking this out on every version of Rick that he can find, but has gone so far that he has no empathy for the Mortys anymore. The great irony is that he takes part in torturing and enslaving Mortys, making him no better than the Ricks he hates.
While Evil Morty’s origins haven’t been revealed on Rick and Morty, his origin could very well be hiding in plain sight in the opening credits. A Morty being abandoned to fend for himself against monsters like that would develop a real grudge, perfectly placing him as someone who would become Evil Morty.