Well he was lucky enough to land on a Fongoid planet, and managed to convince the gullible Fongoids he was a sign that the Zoni trusted the Fongoids once again. After this he probably got them to reveal the (no longer) well kept secrets of the Zoni to to him. This resulted in a meeting with Orvus being arranged, which ended in a disaster that he probably didn't share to the Fongoids. He was probably like "Right, well Orvus said it's all good, and I can return to the Great Clock now. Anyone care to tell me where that is exactly?"
The Fongoids probably know this information, but have sworn to never disclose it or even hint at them knowing anything about it. But this batch obviously trusted Nefarious quite a lot. They probably wouldn't tell Ratchet because there is no sign that he can really be trusted with that sort of information.