M. Night Shyam-Aliens! is one of the trippiest episodes of the series, which makes it pretty ripe for interpretation. This is the one where Rick finds himself inside of a Matrix-like simulation on an extraterrestrial spacecraft. The idea being that the aliens want to trick Rick into giving up the formula for concentrated dark matter. Jerry is there too for basically no reason other than to Jerry it up in a simulation that really only had the capacity for Rick.
Eventually the gang "escapes" the simulation... only to realize that they were in a simulation INSIDE of a simulation -- which included a fabricated Morty.
One of the early hints that is never directly called out is Jerry's tuxedo. Note that, in the initial fake "escape" out of the first dimension, Jerry is still wearing his simulated suit. It's not like he wore a tux to the spaceship, so he shouldn't be wearing it if he had really made it out of the simulation. This turns out to be the case during the "real" escape, as Jerry is left in his tightie-whities when the simulation ends and fake-Morty disappears.
So that's the real world, right? Well, maybe -- and maybe they're still in yet ANOTHER simulation. See, when Rick and the fake-Morty are running around, they come across this big Matrixy room full of aliens hooked into what looks like a simulation (though at this point, they are still in a simulation). The various shapes of the aliens are a little hard to make out, but we get a good look at one creature in particular.
The same alien appears later in the episode (in yet another simulation), but they actually show up in episode nine. They turn out to be Plutonians, citizens of the totally-not-a-planet Pluto.
As the theory goes, the fact that we're seeing these made-up aliens in the first place -- and the fact that we zoomed in on these aliens in particular -- is a clue that Rick and Jerry are both still in a high-tier simulation. There was no big wedding crash, there was no time stoppage, and Mr. Poopy Butthole is indeed not real. It's not a world any of us want to live in, but there it is.
Most episodes of the show are pretty compartmentalized, but there are some pretty sneaky details for those willing to look hard enough. Earlier in 2016, the YouTube channel The Save Point Guild put together a pretty convincing case using those kinds of particulars -- and if it's true, it has vast implications for the rest of the series.
We've already been over Rick and Morty's copious usage of alternate realities in its storytelling, but the episode "Mortynight Run" is a special case that may or may not prove that we don't follow the same Rick and Morty for every episode of the series. In fact, we might have switched dimensions within an episode without even realizing it.
The Rick and Morty that we would consider "ours" belongs to the universe designated C-137. Whenever we see the characters refer to that specific code, we know that we're dealing with the same grandfather/grandson pair that we're used to. But there are several episodes where we don't get this specific universe name callout. Yet, what makes Mortynight Run so important is that when checking Jerry into the interuniversal daycare "Jerryboree," we do see that the characters come from C-137. It's right on the sign-in form.
Also crucially important here is the ticket they get for their Jerry, which appears to read "5126." Without that stub, Rick and Morty wouldn't be able to tell which of their sad bags of crap to pick up when they're done with their adventure.
After this moment we get the bulk of the episode. Morty foils an assassination attempt on a gaseous being, accidentally murdering hired killer Krombopulos Michael in the process. This inadvertantly leads to tons of people being killed in the collateral damage of Morty's escape -- and he ends up killing the gaseous being on a faraway planet anyway. These events aren't really integral to the theory, except for the part where Rick grabs up some unique green crystals.
Remember those green crystals, we'll get back to them later. We wouldn't dare take a large screencap and paste it on the page just to pad out the article. Well, we aren't doing that right now, promise.
After Rick and Morty return to pick up their Jerry, they stop and chat with a couple of their other selves. Turns out, not all Ricks and Mortys had such a harrowing day -- some of them just hung out at the arcade. Then, just as they're picking up their Jerry, another Rick and Morty arrive.
The Rick holding the ticket only just came onto the screen, but he's asking if they have Jerry-5126 -- which could only mean this "other" Rick is the one from the C-137 universe. At some point, we switched universes, meaning that for most of the episode, we were not following the same Ricks and Mortys that we've seen for the rest of the series. Or have we?
With this revelation, we now have to believe it's possible that any given episode of Rick and Morty that doesn't specify that it takes place in C-137 could take place in any number of universes. Using this information provided, we can actually point to one episode that takes place in the same "alternate" universe as the one from Mortynight Run. Remember the Mr. Poopy Butthole episode?
In "Total Rickall," which takes place two episodes after Mortynight, Rick and Company are besieged by imagination parasites that make everyone believe they've been family friends the whole time. The intro to Total Rickall is striking, because it retroactively adds in a character called "Mr. Poopybutthole" to scenes in which he was not otherwise present. Given the context of the episode, it seems obvious that Poopybutthole would be an imagination parasite, but he turns out to be real. Which means that everything that we saw in the intro actually happened , which means that Total Rickall takes place in an entirely different universe.
Which universe? Well, early in the episode Rick is seen doing this:
Those rocks Rick just threw away appear to be the very same unique green crystals that Rick stashed in his ship back in Mortynight Run. Which means that we may be looking at the same universe in which Morty killed Krombopulos Michael, a bunch of random civilians and a sentient gas cloud. It's definitely not Universe C-137, but there's not a firm name for it. I propose "The Mr. Poopybutthole Universe." If only to get more chances to say "Mr. Poopybutthole."