One of Rick and Morty's best serialized storylines is the mystery of "Evil Morty," the alt-dimensional version of Morty that was revealed to be an evil super genius at the end of S1E10 "Close Rick-counters of the Rick Kind". After successfully programming Evil Rick to assassinate dozens of other Ricks across the multiverse, Evil Morty escaped into the crowd of orphaned Morty's living at the citadel, never to be seen again.... until this season.
After Rick brought down the Citadel in the season 3 premiere "The Rickshank Rickdemption", S3E7 "The Ricklantis Mixup; Tales from the Citadel" explored what Citadel life was like after its fall, and the growing schism between the Ricks and Mortys living there. The episode of course ended with the biggest twist we've seen in the series so far, when it's revealed that an unlikely Morty who becomes president of the Citadel, is actually Evil Morty!
Now that Evil Morty has the power of the entire Citadel behind him (and has slaughtered any opposing forces), it seems as though Rick and Morty has officially crowned the show's 'Big Bad.' However, we still don't know much about Evil Morty, but clues being pieced together by dedicated fans point to an origin story for Evil Morty that could change the entire premise of Rick and Morty as we know it...
The most popular (and evidenced) theory is pretty simple: Evil Morty is actually Original Morty (i.e., the real Morty C-137).
One of Rick and Morty's staples is replacing main characters with alternate versions of themselves whenever it becomes convenient: like in S1E6 "Rick Potion #9", when the majority of the original Smith family (Jerry, Beth, and Summer) was left stranded in a dimension that Rick and Morty accidentally "Cronenberged." That's all to say: it's been established in the show that one of Rick's go-to moves is getting a fresh do-over by simply hopping to a new dimension, leaving some serious resentment in his wake - such as when the Original Smith family left behind in the Cronenberged uinverse turn savagely against all things Rick (see S3E1). That's where Evil Morty comes in.
Rick and Morty has continuously dropped some nice Easter egg references to Morty and Rick's relationship before the series actually began. In both S1E10 "Close Rick-counters..." and S2E5 "Get Schwifty," we see imagery of Rick spending time with a baby version of Morty - first in a recalled memory of Rick's, then in a photo that Bird Person keeps on his wall.
These are big clues, since the entire premise of Rick and Morty is that Rick returns to Beth and the Smith family after a twenty-year absence. That would mean Rick left six years before Morty's birth (he's currently age 14), making any images of Rick and a Baby Morty totally anachronistic.
...At least in that timeline.
Now we get to the meaty part of this Evil Morty theory:
If Rick has memories and memorabilia of a baby Morty, that's pretty big evidence that the Morty we've followed throughout the series is not the real counterpart to Original Rick, and that the premise of the show has always been complete B.S. In reality, the Rick who left Beth at a young age never returned, and Original Rick (C-137) simply stepped into a void that universe's Rick left behind, for a trademark "do-over" attempt to reconnect with his family, just like he did so casually in "Rick Potion #9".
So what's the real story of Original Rick and Morty? Well, that's the show we've never gotten to see, but may eventually get in a revealing episode or flashback.
Basically, the clues point to this: In the dimension and storyline that Original Rick actually comes from he stayed with Beth and his family, thereby changing the entire dynamic of the Smith family. Rick was around to truly bond with this grandkids as a father-figure (sorry Jerry), and that influence helped Morty grow up to be a genius like Rick, instead of a insecure cowardly mess. However, at some point, it seems that Original Morty (aka Genius/Evil Morty) had some kind of big falling out with Original Rick, causing them to split. As Original Rick has been trying to rebuild family connections by taking up residence in alternate timelines, Original Morty has become Evil Morty, intent on some larger plot against Rick and the Citadel that has yet to be revealed.
Rick hints at this all being the case in "Close Rick-counters..." when he cautions Morty against arrogance, saying, “A cocky Morty can lead to some real problems. It can be a real bad thing for everybody.” Rick says the line with a gravitas of experience in his voice, suggesting that he has seen an arrogant or imperial version of Morty go dangerously bad - probably the same Morty he himself once trained!
If this origin theory turns out to be true, it changes viewers' entire perspective on the show, and leaves room for a big flashback storyline set in the actual "Original Rick and Morty" universe, as well as room for the current Morty to undergo serious character growth (i.e., fulfilling his potential as a rival to Evil Morty). So how likely is the theory?
While this vesion of Evil Morty's origin is certainly popular, Rick and Morty's showrunners aren't exactly creating a LOST-style puzzle, here. As co-creator Dan Harmon explained to EW recently, the clues about Evil Morty (or any of the show's mysteries) are meant to be open-ended, until the showrunners themselves decide on the path to take.
As Harmon put it:
"We never want to commit the crime of thinking so far ahead that we paint ourselves into a corner, but it would be equally foolish to throw things out there without thinking about them that we then realize two years later, “Jesus, if we hadn’t done that, we could be able to say that everyone’s a robot!” So we take it kind-of seriously. We make sure there are multiple possible answers."
If there's one thing that Rick and Morty excels at, it's skewing or outright skewering expectations, as well as totally mocking story elements that other shows would treat with reverent importance. Considering the way that Rick has casually replaced major characters or rebooted the entire setting of the show, the reveal of Evil Morty's origin could end up being treated as a minor thing - or better yet, a prime opportunity to mock fans for their over-indulgence in theory, rather than actually enjoying the journey of watching the show.
Knowing Rick and Morty, the origin of Evil Morty is not a mystery the show will rush to answer, and that's okay with us. There will be plenty of other fun to have while we wait for that big reveal.
Rick and Morty is currently finishing up Season 3. It airs Sundays @ 11:30pm on Adult Swim.