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There are 40 Zoni in Ratchet & Clank Future: A Crack in Time, but only two are known so far on Ratchet & Clank wiki's article.

These are both at Krell Canyon:

  1. After you boost to the canyon with your hoverboots, turn right and after a couple of seconds there should be a hoverboot launch pad on your right side. Use it to boost you to a Zoni.
  2. There is a battery bot in a hover booting section of Krell Canyon; it is placed near a vendor. Take the bot and throw into a nearby slot. Inside, there should be a Zoni.