His back story is the same as the canon series. Being the lead scientist of Project Paradox to create a time machine, an accident causes him to get sucked into the time stream. He becomes immortal, and wields the Chrono-Navigator, allowing him to travel to any time in any dimension.
Paradox appears when a Trans-Dimensional Monster appears, threatening to destroy the Earth. John, Gwen and Kevin meet him, and manage to reverse the incident of the Trans-Dimensional Monster. Since then, he appears in world threatening incidents and time events. He assists in the battle against the Highbreed. After John accidentally unlocks Clockwork and travels through time, Paradox tells him to keep it secret. After John's death, he gives a cryptic idea to Julie to go back in time.
He appears when Eon attacks John 10,000, and assists in stopping him. He also gives John a positive message that things will get better. He returns after beating the mind controlled Winston to restore the Omnitrix.
As Aggregor makes it to the Forge of Creation, Paradox assists the team in getting there. He then congratulates them afterwards for their victory.
When Aggregor returns on Solaris, Paradox takes John to the incident where Iblis and Mephilis were created. He gives John the warning, and takes him back. After Solaris returns, Paradox says that he is powerless. He manages to open a portal to Earth, allowing John to get some past and future help.
Paradox meets Lucina in the future after Malware goes back in time. He sends her back, and says that he got reprimanded for doing so.
After the Olympus event, John finds him in the Underground of Greece. He explains that he sealed away the Greek gods, the history of Gaia and Phantom, and him losing his powers to Gaia. He had Rook assisting in fighting Gaia. He also formed a romantic relationship with Hestia.
An earlier version of Paradox comes to John after he lost the Omnitrix. He tells him how Gaia had been spread across the dimensions. He returns after John finds out how to stop Gaia permanently.
Paradox appears as an ally, helping Chopper and Kevin when they are alone. He saves them from a blizzard, and then tells them about the others being in jail. His powers here are fueled by Clockwork, which he willingly gives to the heroes. He doesn't meet with John.
Paradox has his Omniverse appearance. Paradox appears to Grey, using his presence to protect the ship they were on from the space time rupture. He tells Grey to lead Ryder to Los Soledad in order to fix it. He appears after Ryder fixes the time stream, telling him that all that was needed was to destroy the time machine.
He returns to take Ryder home from Megaman's dimension, telling Megaman that he will need help from those he considers powerless in the future.
He approaches Ryder after the Trans-Dimensional Monster appears in Ryder's time, revealing that he knows that it is his assistant Hugo, who accidentally got sucked in. He recruits Ryder to assist in saving Hugo, and they combat against Eon who wants to kill the Young Paradox. They defeat him and erase his memory of the events.
Paradox arrives in Jane's dimension after her first official encounter with the Grimleal. Jane asks him to take her to the time of her incident, but Paradox blatently refuses, saying that it was too much of a risk. This angers Jane, as he speaks to Max.
Paradox appears to warn John of the eventually return of the Organization. He gives John the idea of forming a team, being the inspiration for the Omni Crew.
