The video opens with Luigi trying to beat Mario's high score on an arcade machine. However, Mario and Toad keep setting off grenades, causing Luigi to get a game over and become mad at the two. Suddenly, the castle's phone begins to ring, and Mario answers it. Calling is Professor E. Gadd, who asks Mario if Luigi could come down to the lab for a cloning experiment. Luigi declines the offer, but Mario decides to visit the lab himself.
Mario then begins looking for E. Gadd's lab, apparently situated in the town of Wet-Dry World. After accidentally stumbling across an octogenarian girl showering in her house, Mario finds the right building and enters the lab. For whatever reason E. Gadd doesn't seem to be there, so Mario starts exploring. Then he comes across a circular apparatus that soon turns out to be a time machine. Mario button-mashes the controller, activating a portal within the aperture of the device's ring. Mario jumps in just as E. Gadd phones Mario again, to warn the latter not to use the device. However, it is too late; Mario has already started warping via the machinery. E. Gadd then laments that he must kill himself.
Mario travels through a time portal and ends up in an old version of Super Mario 64. Everything is in sepiatone, and the castle's residents are not yet familiar with the plumber. Mario chats with Toad for a bit, presumably introducing himself for the first time; he then begins playing some retro games to a Scatman John chiptune. Mario then expresses his boredom and decides to visit another time, 1966.
Now at Nintendo HQ, Mario says that wants to see how SM64 was made in the first place. A Toad Guard in the lobby notices him and asks what he is doing. Mario says he needs to go to the bathroom, but also gets the Toad to reveal that the Nintendo staff are, as Mario expected, having a conference. After emptying his bladder, Mario devises the perfect plan for entering the conference unnoticed – smashing through every wall in his way. Meanwhile, the Nintendo boss starts a brainstorming session for a new Mario game, but nobody has any ideas. One of the employees needs to go to the bathroom, and leaves the upper hallway to go to a different restroom than Mario used. Just as the staff member suddenly gets the idea for Super Mario 64, Mario crashes through the second-story bathroom's wall and kills him. Mario realizes that he landed on a person, hopes that it was nobody important, and quickly escapes the building via a painting. The Nintendo boss then goes into the bathroom and notices the corpse, stating that it means the dead staff member won't have any more ideas for the project.
Mario runs away from the building and notices the fabric of reality beginning to glitch away and dissolve. He then triply warps back to the present time, only to find whatever SM64 map he landed in nothing but a black void. Mario asks if anyone else is alive, but realizes due to the lack of a response that the other SM64 characters and objects must never have existed in the first place. However, he deduces that SMG4 must still be around. Mario calls out to SMG4, who turns around, revealing that he only has one hollow eye socket for some reason. Mario freaks out, prompting Glitchy to ask whether he knows Mario. Mario explains that SMG4 is his boss and that the latter makes Super Mario 64 Bloopers, but to no avail; SMG4 states that he knows a Mario – maybe from an earlier game – but not one that works for him. He then says that he only makes Zelda 64 bloopers, causing Mario to freak out further. Mario tries to run away, but slides down an invisible slope, prompting SMG4 to call the former nutters and go on to watch MM54321's OoT Bloopers. Mario then resolves to go back in time and fix everything.
Back at Nintendo HQ, the boss is holding a somewhat half-assed funeral for the dead staff member, despite not one of the staff caring about him at all (other than Yellow Guy, an employee reduced to tears by the loss). As Mario arrives on the roof, the boss laments how the dead staff member never gave any good ideas, and invites the others to look at the corpse as if they cared. Mario then throws 1UP Mushrooms down to the funeral in an effort to give the dead worker an extra life. They begin chasing the staff members; Mario runs past the corpse, causing the mushrooms homing him to revive the dead staff member. Miraculously, the now-revived Nintendo employee has his memory intact, and relays his idea for Super Mario 64 to the boss.
Now back home, Mario and Toad begin using grenades once more, which causes Luigi to mess up at his game again.
As this episode centers around time travel, there are bound to be several related errors.
The black void world in SM64's place should not exist, for the sole reason that the employee's revival – and later, the development of SM64 – causes a stable time loop. This means that SM64 would always exist, because the employee's death, funeral and revival are in the same timeline. However, had the void not exist, Mario wouldn't have had any motivation to fix the mess he made.
It is unknown why SMG4 is a soullessly-eyed cyclops in the void world, nor why he exists in that world at all.
It is also unknown how anything, including floors, slopes, and collision data, much less characters, can exist at all in a realm of non-being.
SMG4's and MM54321's screen names are unchanged in the void-world universe, despite them more likely being SZG4 and ZZ54321 (or something radically different) due to the fact that they make Zelda bloopers instead.
E. Gadd's lab should not exist in the universe where SM64 does not exist, due to the fact that it is seemingly located in Wet-Dry World.
Mario can visit times in SM64's in-universe history, as well as real-life history. How this is is unknown.
Why retro SM64 is in sepiatone is unknown. Mario observes the world as sepiatone, meaning that the effect is not due to the camera.
Adding on to this, nothing is in sepiatone during the Pac Man and Tetris sequences, despite Mario being in the same time period as the last scenes, and being sepiatone there.
Mario sometimes time-travels without going back to the time machine, or at least not doing so on-camera.