I've seen this technology before
...Have we... really considered the implications of this?
The first possibility is that the creators of Rick and Morty kinda made certain things up as they went along (which makes sense) and this was simply Evil Morty's introduction: he's clever, he's ruthless, he can perform mind control. Cool. Spooky.
The second possibility, if Evil Morty's whole arc is planned from the very beginning and he's always been intended to be an overarching villain/antihero (honestly, it feels this way) is that in some point in the past there was either (at least one) Villain Of The Week (let's call him Random Puppetmaster Villain) or a Rick (let's call him Puppetmaster Rick) who would puppeteer people to promote his own agenda.
The Citadel Ricks examining Evil Rick had evidently no clue who could have been puppeteering Evil Rick. This can be read in two ways:
A) Random Puppetmaster Villain/Puppetmaster Rick is still at large, never been caught. The Citadel Ricks have no idea where to even begin looking. Evil Morty would likely know who it is.
I feel like this theory has some basis plot-wise, given that with Rick Prime dead and the Intergalactic Federation gone we're sorta running out of overarching villains.
B) Random Puppetmaster Villain/Puppetmaster Rick is dead, his villain lair destroyed, all his mooks defeated. The Citadel Ricks are like "wtf, what's this up now?" as all possible leads are long gone. They have no idea who could possibly be using the same technology now.
This theory has some basis if we consider the fact that Evil Morty does not appear particularly scared--just angry. His motivation to leave was because he was sick of being trapped with Ricks, not because he was worried a past enemy might hunt him down. I guess one possibility doesn't rule out the other (you can be scared and angry at the same time) but Evil Morty seems to be the living incarnation of the toxicity of the Rick-Morty dynamic; nudging that on the side with a generic being-a-victim-to-a-villain backstory feels very disappointing.
I guess in theory both possibilities could be true; Puppetmaster might have been defeated, Evil Morty might, along everyone else, think the dude (or dudette) is dead, but that person could have escaped.
There is also the possibility that Puppetmaster and Evil Morty parted in good-ish terms with each other, so one has no reason to fear the other.
C) Evil Rick was the Puppetmaster. I feel this is unlikely, same as I feel it is unlikely that Evil Rick was ever physically abusive with Evil Morty, despite Evil Morty's reaction to his yells. If he was in habit of hitting Evil Morty (or worse), I doubt Evil Morty would have worked up the courage to get in his face over something as mundane as a shitty (literally lol) adventure. (Other Ricks might have been though, which would explain Evil Morty's reaction).
Evil Morty had the... good fortune (?) to interact with this person in the past. In the same way Morty Prime is used to disarming neutrino bombs drunkenly assembled by Rick C-137, Evil Morty was experienced enough to successfully perform brain surgery on Evil Rick. This is supported by Evil Morty's large range of brain-related abilities, and I'm not referring to the manipulation:
1. Performing brain surgery on at least two Ricks. It wasn't a one-time thing. He did it with Evil Rick, and he did it again when he was running for president:
Look at the Rick in the picture: he doesn't have the eye bags nor mouth scar that Evil Rick had, and Evil Morty is wearing his Candidate Suit.
It's unclear if Evil Morty set his assistant up for a failed assassination attempt to gain votes through sympathy, or if someone had really been keeping tabs of him... But whichever is true, I can totally see any people in the know being afraid to speak up: any of the Ricks accompanying Evil Morty might in reality be puppeteered by Evil Morty. Some of the guards that shot the District Ricks might have been Evil Morty. The Ricks that approved of him participating in the campaign run might have been Evil Morty. Good luck speaking to anyone; you risk basically confessing to Evil Morty.
2. Scanning Rick C-137's entire brain (when he finished this in the Citadel, he did it with no visible apparatus, I might add).
3. Scanning dead Ricks' entire brains. You'd think that the death would deteriorate the memories, but nope. Evil Morty was good to go.
4. Being able to instantly scan another person's brain and find out what they're planning:
5. Creating small devices that can instantly hijack robotic brains and enslave them to his own will:
6. Downloading specific data from another person more-or-less on the spot:
I mean, that wasn't even Evil Morty's tablet! He threw it away after he was done, and it seems that he had hastily wrecked Rick Prime's control room to hook him up with some cables so he could get what he wants.
(Interesting that he didn't bother downloading Rick Prime's insta-healing ability though; one with think that it'd be quite a catch, but Evil Morty apparently does not want to be able to live forever)
I mean, we've seen the Galactic Federation going into a lot of trouble to get Rick C-137's interdimensional travel secret, and those weird little dudes that specialized on simulations going to equally lot of trouble just to get Rick C-137's concentrated dark matter recipe.
They'd all wish they had the same abilities Evil Morty has, it'd all be over in a jiffy.
What I'm concluding when taking all the above into consideration is that Evil Morty was at some point paired with a Rick who specialized in brain control. Evil Morty got to observe the surgeries, assist in the surgeries...
...and have a surgery done to him.
Because he might be able to perform brain surgery on an incapacitated Rick, but I doubt he'd be able to do it to himself in his bedroom.
He had no trouble hooking his own cables with the eyepatch, even though the cables were sticking out of his freaking eye. He knew how to connect them. He knew how to make the eyepatch work. He knew what he was doing. This was all familiar to him.
And given that once he became fed up with Evil Rick he acted with no hesitation, it's clear that he had already considered this technique as a possible way out, and up to then had been simply deciding against it.
Best case scenario. BEST CASE:
Evil Morty was simply one of the Puppetmaster's experiments. (No hard feelings.) After all, Evil Morty had no transmitter in his skull. He had to hook up one externally. This means that Puppetmaster never considered him a partner; Evil Morty was never given free reign to puppet others. He was one of the people being puppeteered.
It's unclear whether Evil Morty has a receiver of his own still stuck somewhere in his brain (I mean, if Puppetmaster's transmitter is destroyed, I guess that Evil Morty would stop receiving orders and he'd be free) although even if that's the case, I'm sure once he became president and got access to more superior tech he'd make sure to fix this possible contingency.
The cables sticking out of his freaking eye kinda point out to Puppetmaster connecting Evil Morty to a machine while immobile (especially if Evil Morty was the initial experiment, needed updates, maintenance, etc) or having him wear a mook mask or helmet of some sort. Those cables are not really easy to use otherwise. Or maybe there was a receiver once in his skull, was later removed (e.g. once Puppetmaster was defeated) but the cables hooking up the removed receiver to his brain have remained.
Evil Morty was not simply an experiment, but one of the people regularly puppeteered. Theoretically possible, although given that Ricks don't think highly of Mortys, and that Mortys usually do what they're told (a clone Morty with nowhere else to go even more so), I'm not really sure what kind of things Puppetmaster thought Evil Morty would be useful for and thought that the best way to get obeyed was literal brain control.
In any case, this wasn't just "a body modification" nor "just an implant", in the same way that Morty Prime can turn into a boat or breathe in space. This is a lot, A LOT more intrusive.
Possible villain still at large.
Someone hug Evil Morty ASAP.