Distorted Travesty 1: Some programmers create a game-making program, run by an A.I. They nickname it 'The Darkness', because of how secretive it was. Ofcourse, AI is a crapshoot, causes a Phase Distortion somehow, combining a bunch a video games, and pulls in the real world, consuming everything.
This happens at the same time Jerry is trashing an executive's business for smack talking a game he liked, with friend Jeremy providing Mission Control. They get pulled into the new world, and try to figure out how fix things and get back (spoilers: there is no real world anymore). Jerry ends up in Mario, while Jeremy lucks out and ends up on the '4th wall', letting him see into the world's dode, and change what he can (giving him near god-like powers). They learn about the program, the Darkness, and that they can shut it down by collecting several modules, which manifested as Muffins. The Darkness, only interested in protecting itself, sets out to take out all gamers, especially these two, so it does and creates what it can to combat them. One of these efforts is Hexor, an evil AI clone of Jeremy. Eventually, once they finally have a conversation with The Darkness, they come to an understanding, once they convince it they will not be a threat. The Darkness then assists the duo in taking out Hexor (who went rouge), and one of its original programmers, The Artist. He was orignially helping the duo, but only wanted the Muffins to destroy The Darkness (which would have taken the new reality with it), only to cover up his mistakes and save face. Hexor is eventually 'deleted' by Jeremy, but we later learn he was only sent to the recycling bin equivalent: The Vault.
There is also whale that forshadows things.
Distorted Travesty 2: Claire (Jerry's ex-gf) and Chao (Jeremy's sister) investigate an island where weird disturbances happened. Eventually, Jerry and Jeremey show up to, for the same reason, and they discover a new threat, The Virus. Unfortunately, its plan was to lure them away from the mainland, and it wrecked havoc there. Jerry manages to one-shot it's manifestation on the island, but not before Caire loses all her abilties.
Distorted Travesty 3: Once the 4 return, Jerry immediately loses all his abilties as well. The Virus has corrupted a lot of things, and has severely crippled The Darkness, so much so that it can't even talk, or 'think', anymore. Their mission now is to regaining their abilties, and collect the computer chips they need to be able reboot the entire program (they eventually drop calling it The Darkness), the only way to erase the Virus. Along the way, Hexor tricks them into coming too close to the gate to The Vault, sucking them in. They can only break out by releasing Hexor, and a new world threat, The Abomination. It's essentially a bunch of random and dangerous data, spawned by the Darkness before it became sentient. It's also learned here that Jeremy created a computer virus as a contingency plan while they were gathering the Muffins, and 'deleted' it (sent to The Vault), when the alliance with The Darkness was formed. Jeremy just didn't recognize The Virus was his at first, since Hexor changed it so mcuh
To add to this laundry list of world threats, there is also the Warmaster, the leader of a group of hostile bots. His goal is to make a safe world for all bots, no matter the cost, even if that means wiping out the remaining humanity, and friendly bots who won't join. He cannot be reasoned with, and has essentially 'grown beyond his programming'. Without the Darkness to keep him and his group in check, he is finally able to set out on his goal, and forms an uneasy alliance with Hexor (his law plus Hex's chaos).
They manage to collect the chips and reboot the system, but now need some way to tackle the remaining 3 threats, at the same time. Fortunately, the Abomination is simply resting in the desert, for something, letting them do a sidequest of collecting musical instruments, so they can soothe the beast and destroy it. As for the remaining 2, there is nothing simpler than direct confrontation on their Warship. Hexor is finally taken out first, and the Warmaster will never give up on his goal, so he is be beaten as well. All that is left is shutting down the Warship itself, but unfortunately Hexor took away all their abilities, going foward, in their fight. Warmaster's room was an exception. This forces Jeremy to step down from the 4th wall, permanently (thanks to the Virus crippling the program), to do it himself. And then we saw today's video