I'll just copy and paste this here and delete the thread I made.

I had the idea that Rick's Morty wasn't the original Morty, and that Morty's Rick wasn't his original Rick but after searching the post history, soni133 covered it pretty well.[1] But for those that haven't come across it, the idea is that Rick dimension travels to escape his mistakes all the time. It is likely that dimensions exist where Rick died or plain dissapeared instead of returning to the family, and that a Rick in trouble from another dimension could easily fill the void. I would like to add that the very first scene in the intro is likely Rick losing his original Morty. Now about the evil Morty from CROTRK... It always bothered me that everyone assumes evil Morty is a Morty at all. After all the whole point of the episode is that Morties are stupid which is why they are useful to Ricks. If Evil Morty is actually a Morty, why bother with building a robot or kidnapping so many Morties. Rick himself says that the whole thing is overkill. This is because Evil Morty is not a Morty at all, he is a Rick in a Morty's body. Rick Trouble in Little Sanchez, shows Rick can move his mind to other bodies. Now I wouldn't want to speculate as to why Rick would do this, but in all the dimensions Rick inhabits there must have been at least one Rick that decided that he needed to get out of a bind by hiding in Morty. As the same episode shows, he may have had no choice except to stay there because his original Rick body probably died. Now how do I know that a Rick is in Evil Morty's mind? If a Morty's value to a Rick is that their stupidity camouflages them, then it is somewhat safe to say that NO Morty is smart enough to build a robot and then control it across hundreds of realities. Much less outwit the multiverse's Ricks by framing the main Rick. If there was no Rick to begin with, why kidnap so many Morties? The brainswap would have made Evil Morty register as a Rick to anyone looking for him. So he still needed a Morty, but was no longer in a Rick body to make kidnapping one in a straightforward way practical. Which is why he would have built the robot Rick. Big Trouble in Little Sanchez offers one final explanation: A Rick in a Morty's body would have easily become unstable. The only reason the main Rick got through it was because of Summer being around. Someone Evil Morty would not have access to or realized he even needed around. Cyborg Rick tells Rick that "the only truth in the universe is that Ricks don't care about Morties". There's only two reasons why Evil Morty would make C-Rick say this. Either he was a Rick, or he was a genius Morty. The problem with it being a genius Morty is that a genius Morty must have a dumb Rick. But Dumb rick already has a Morty. Evil Morty, would have easily been able to escape undetected with the horde of dumb Morties around him. Sub-theory: I believe that Cyborg Rick lies when he tells Rick he will download his brain contents and then kill him. I believe that he was going to download Rick's brain, wipe the mind clean, and transfer the Rick inside Evil Morty into Main Rick's brain. He would have gotten away with it too if it wasn't for those meddling Morties! Suddenly what was going on in CROTRK, makes sense. A Rick put his mind in a Morty. Alone and trapped in a teenager's body, he went nuts and in a fit of self-loathing/Morty-hate he kidnapped all those Morties and made a point of torturing and imprisoning them in order to put his plan in action. A plan that would see main Rick framed, go on the run, and find him, in order for him to steal main Rick's body. After the Morties escape, the attention goes to the dead cyborg Rick and Evil Morty is able to make his escape. TL;DR: Evil Morty is actually Rick after a long time trapped in a teenage body. The only thing I don't really get, is whether "The One True Morty" was an intentional part of his plan or whether it was an unfortunate oversight. It may very well be that Evil Morty's disdain for Morties was strong enough to blind him to a potential insurrection.