Donatello and Cody manage to trap Viral in a battle dummy. When she fails to defeat the Turtles, Sh'Okanabo punishes her by refusing to repair her or free her from the battle dummy. Viral later serves as Sh'Okanabo's minion. In the episode, The Gaminator, Viral executes a failed plan where she traps the Turtles' minds inside the Gaminator program where she attempts, and, once again, fails to defeat them. In that episode, she demonstrated the ability to phase in and out of the physical world into the computer world.
Viral managed to create a copy of Cody's time-window to send Earth into an unspecific time-period. However, the device wasn't powerful enough and caused rips in time all over Earth. When Cody shut the window down, he notes the specifications and when he asked what she was trying to do, Viral left the scene.
Viral survived the destruction of Sh’Okanabo's lair and assisted her master in taking over Moonbase Bishop. When the Turtles and President Bishop were captured, Viral partially explained her master's plan to use the Atmospheric shield around Earth to completely leave it in darkness. When Cody and Serling came in and rescued the captives, Viral went ahead to take control of the Solar collection grid. She almost succeeded in covering the Earth in eternal darkness when she was tricked into Serling, caught in a decompiler, which dissected her data bit by bit.
However, Viral had a number of failsafes that restore her scattered data at least 97%. She observed the Turtles preparing to return to their own time, so she takes control of Serling and disrupts the window, causing the Turtles, Splinter, and Serling (whose defense protocols were deactivated) to fall back into the Mesozoic. But when they defeated the Spinosaurus, she sent them to the Dark Ages, where knights attack them. But Mikey taunted Viral into taking them somewhere more technical, but she took them to the not-so distant future, where the Foot are fighting among each other, each represented by a different incarnation of the Shredder: the Utrom one, the demon and an entirely new one. But Donatello used a coil from the Utrom Shredder's exo-suit to reboot Serling, using his decompiler to once against destroy Viral. But as they race back to their proper time, a part of Viral appeared in Serling, using the decompiler on the other Turtles who were not inside (as in the time stream they are temporal data). But Splinter takes the blow just as they return. Viral then escapes from Serling into the Internet, where she attempts to locate a better power source to help her recharge and finish off the Turtles. She finds a data vault belonging to the Foot, which she tries to access but its encryption is complicated and she gets infected with it, her program rewritten and form reformatted, as out of her body bursts the new Shredder, the Cyber Shredder.
It is later revealed in the season finale that Cyber Shredder had inherited many of Viral's digital properties, such as her digital core, which enables her to escape harm. This allowed Donnie to figure out a way to decompile the Shredder, putting an end to his newest incarnation and Viral for good.