The Zoni dimension was the home of the Zoni. When the Great Clock was built, approximately 117,000 of the Zoni species, including their leader, Orvus, moved there to protect it and watch over space and time. In order to survive in other dimensions, the Zoni had to wear robotic suits, as they were beings of pure energy.
A revived Captain Slag, sharing a body with the undead Captain Darkwater who had once been a friend of the Zoni, attempted to travel to the dimension by using the Fulcrum Star to pillage it of the vast riches that were said to be in it. Slag and Darkwater failed to do so at the hands of Ratchet, friend of Orvus's son, Clank, who he was trying to rescue from Dr. Nefarious. The villainous doctor was using Clank to access the Orvus Chamber in the Great Clock and control time.
The Zoni attempted to stop him from doing this, but were forced to flee when Dr. Nefarious unleashed his Hypersonic Brainwave Scrambler on them. The device caused a great deal of damage to the clock and forced the number of Zoni in the facility to drop to 305, and then to 120. Eventually, all Zoni in the facility had fled, many presumably back to their home dimension. 40 were scattered across the Breegus System; these were all collected and saved by Ratchet using the Zoni Vessel and returned to the clock by him personally. It is unknown whether the 116,960 remaining Zoni ever returned to the clock on their own.