Shredder had already the second piece of the Eye of Sarnath, but had to hook it to a computer to unleash it's powers. He and Baxter Stockman broke into a high-tech lab, and found O.M.N.S.S. and attached the second piece to it. Now under the command of Shredder, O.M.N.S.S. tried to destroy the Turtles by sending self-driven vehicles after them, and later taking over the TurtleVan and tried to crash them, but they managed to stop it.
Shredder wanted to use O.M.N.S.S.'s powers to open a portal to Dimension X and get back his Foot Soldier, not longer needing the help of Krang. However the Turtles arrive and April shuts down O.M.N.S.S. by simply pulling the plug. Shredder and Baxter unfortunately escaped.
OM.N.S.S. was an intelligent and arrogant machine even before it was connected to the fragment of the Eye, capable of directly affecting its environment. It seemed to take offense at Baxter's dislike of intelligent machines.