The series began in 2009 as a Stargate-based story featuring two Ancients as they live as ascended beings. This story was eventually ended when the Ancients caused two "Apocalypses of All Existence"(the end of the universe), thus rebooting the series into its current status.
These Apocalypses have occurred several times throughout the series and are mainly used by the creators as a way to recreate the RPG in new form. Despite these attempts, the 3rd universe format has endured.
This plot featured Tim as a peaceful scientist and explorer whilst his counterpart Rushy was the main villain and mad scientist. Even though insane AIs had been a recurring gag for some time, it never became a major plot point until the introduction of Eridanus, an extremely intelligent and diabolical computer virus(originally a computer network) that took Rushy's place as the main villain.
At that point, Rushy's sociopathic behavior was significantly toned down and he became permanently friends with Tim with only occasional relapses into villainy.
For a while after the demise of Eridanus, the show remained without a main villain until the (re-)introduction of Henry, the administrator of an ancient facility that continued to create varying clones of Rushy and Tim(different species, mindset etc.) thus explaining their reincarnation every time the universe ends(though the reincarnation of the other characters is still a mystery).
It was explained by Henry that mysterious beings from beyond the multiverse created the facility during the 1st universe(when the RPG was still Stargate-based) to make people who would constantly break the Laws of Time(drastic temporal alterations apparently being their energy source). Using their powers, these beings had allowed the facility to survive for approximately 500 trillion years. At that point in the story, the beings no longer require Rushy and Tim so the facility was shut down.
Two pairs of the duo(ponies from My Little Pony and Time Lords from Doctor Who) worked together to transfer the functions of the Paradox Machine into an advanced fob-watch which allowed the characters to directly control their timeline. The device was used to remove Henry, the facility and the rest of the Rushys and Tims from existence.
During the course of the story, both Time Lord Rushy and Time Lord Tim regenerated. Both also changed their names(Rushy becoming a woman named Emma and Tim becoming Philip). The pony versions were magically restored to their original selves.
Both pairs returned to the Fiction and tried to finally return to traveling, but they were quickly intercepted by the Cybermen. Fearing death, Rushy brought Davros, the creator of the Daleks(from Doctor Who) via the gauntlet and had him construct Daleks to protect them.
Working alone, Timothy destroyed the Fiction(trying to undo all the damage they had done to the universe in despair) but he was caught by Davros and locked inside a prison cell with Emma. There they remained until freed by Philip.
The group met up with the Cybermen who had originally attacked the ship and learned from "Cyber-Rushy" that an unknown force had caused the Apocalypse Of All Existence(marking the first time an outsider had done this).
Rushy(now normal again) figured that since their paradox had persisted through six Big Bangs, it would have the imprint of a healthy reality on it. To stop the Apocalypse, Tim and Rushy took a TARDIS and destroyed the Paradox Machine inside a center halo, spreading the healthy reality everywhere while at the same time, wiping them from time and space.
The timelines were fortunately restored when Halsey, a former associate of theirs happened to recall their existence(essentially dragging them back to life). Tim ended up with her whilst Rushy was kidnapped by the Machine Cult. Trying to save him, the other two were captured and forced to open a satellite containing original Eridanus programming, bringing him back as well.
Soon after this, the duo were cloned again, by an unknown force. These clones are capable of time travel and so forth. They soon met up with a danger from a parallel universe in which Tim and Rushy returned to Equestria. Since the threat of the Scourge was upon them, several parallel versions of the duo teamed up with the Elements Of Harmony to venture into the End Of Ponies and save the pony version of Rushy from the Scourge.
The plan included uniting three center haloes via Paradox Machines to open a time rip that took them into the parallel world and time. There, they attempted to change the timeline and stop the Scourge from ever infecting Equestria, but the plan backfired, sending the Scourge throughout the entire multiverse.
The RPG has a number of running gags that happen to come again and again. With the change in series style though, most of these are no longer valid.
- Rushy dying and coming back to life somehow, usually by creating an AI version of himself, cloning, time travel or by the Apocalypse.
- Rushy drinking UED and going temporarily nuts.
- The Fiction being trapped inside a center halo(usually by Rushy's hand).
- A computer turning sentient and then sociopathic.
- Rushy betraying Tim for either his own purposes or cabin fever.
- A center halo, Paradox Machine or the End Of Ponies(a mysterious possible future event) being the explanation for a solution.
- Andrew randoming popping into existence for no apparent reason.
- Tim randomly breaking the forth wall when things get annoyingly cliche.
- Writer Rushy messing things up for Writer Tim when he's trying to be funny(Because I usually have no idea whether or not you're running a plot - Signed Rushy). (Even then, you still mess things up. Signed - Tim)