Quantos, Zolar Forest
- Two Zoni appear after recovering the Zoni Vessel in the Temple of Zahn. The first can be captured immediately.
- The second Zoni must be pursued back through the Temple. It can be caught when you return to the first room.
- The last Zoni is in the Armory, after Vorselon's ship leaves.
- Phylax Alpha : Use the bolt crank near the building to unlock the door and get the Zoni inside.
- Phylax Beta : Get to the end of the linear path.
- Phylax Gamma : Get to the end of the linear path.
Torren IV, Molonoth Fields
- After speaking to the giant talking head, go right. A Zoni will appear near the spring platform.
- A Zoni appears on the Hoverboot course after the final exam. It will lead you on an alternate path, back towards your ship. When you arrive, it will be waiting beside your ship.
Axiom City, Terachnos
- The first Zoni will be visible immediately upon landing in Axiom City. Follow it, and do not let it out of your sight. After a few Swingshot targets, it'll stop on a platform.
- In the eastern half of the Spaceport terminal, there is a barrier that goes down after the battle with Nefarious's droids. There is a Zoni past the barrier. Follow it to the other side of the terminal.
- After clearing the Spaceport terminal, a Battery Bot appears. Grab it and enter the transport tube. At the other end of the path is a receptacle for the bot, which releases a Zoni.
- Vela Alpha : You will need the Hoverboots from Torren IV. Take the left fork at the first intersection and follow the path to the end.
- Vela Beta : You will need the Hoverboots from Torren IV. Get to the end of the linear path.
- Vela Gamma : Chase the Zoni. On the minimap, it will be a white dot that pulses yellow rings. Catch it when it settles down.
- Vela Delta : Get to the end of the linear path.
- Vela Epsilon : Get to the end of the linear path.
Lumos, Krell Canyon
- After you boost down the ramp and into 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.
- Near the launchpad mentioned in the previous section, you will see a blue X jump pad. Jump onto it and follow the path to a high plateau where a Zoni resides.
- By the upper-right (on the map) rock formation in Krell Canyon, there will be a Zoni waiting for you. Follow it through the hoverbooting section to grab it.
- After receiving the OmniSoaker, in the Vogal Caves there is a room with two doors blocked off with tentacles. Suck up some Breegus nectar and fire it right onto the tentacles of the first door you see to cause them to retract. The Zoni lies beyond them.
- Complete "Armageddon Out of Here" in the Bronze Cup.
- Complete "Fun with Fusion Turrets" in the Silver Cup.
- Complete "Endangered Species" in the Gold Cup.
- Complete "Fireproof" in the Raritanium Cup.
Zanifar, Tombli Outpost
- One Zoni appears next to the escaped Fongoid, in front of the ivy door.
- The next Zoni awaits right in front of the security tower door.
- Korthos Alpha : Chase the Zoni. On the minimap, it will be a white dot that pulses yellow rings. Catch it when it settles down.
- Korthos Beta : Use the map to find the spring platform needed to get onto the raised walkway. Follow it to the end to get the Zoni.
- Korthos Gamma : LGet to the end of the linear path.
- Korthos Delta : Get to the end of the linear path.
Vapedia, Valkyrie Citadel
- After you use the first Hover Bolt, do not jump off the first Jump Pad. Instead, drop down (Circle or R2 seems to work best) and find the Zoni on the island.
- In the room between the second and third training courses where you fight a bunch of Valkyries, a Zoni will appear with a group of them on an elevator.
Nefarious Space Station
- At the beginning of the level, head west. After the swingshot section, use the Omnisoaker to cool off the red-hot platforms with water, then take the Hoverboot course to where you can fill up the Soaker with oil. Use it to clean the bolt crank, turn the crank, and follow the Zoni back to where the vendors are.
- Bernilius Alpha : Get to the end of the path. When on the moving platforms, you will need to first get off at the second platform you see to get some oil, then take the platforms all the way around back to the platform with the rusted catapult.
- Bernilius Beta : Follow the string of teleporters to a raised walkway where the Zoni resides.
- Bernilius Gamma : Get to the end of the linear path while avoiding the ice crystals orbiting the moon.
- Bernilius Delta : Fight your way through the level and get the Zoni at the very end.
Morklon, Gimlick Valley
- After defeating Argos, you will return to the new present-day. In the westernmost raised section of the village, you will find a Zoni.
- Corvus Alpha : Follow the linear hoverboot and swingshot course and grab the Zoni at the end.
- Corvus Bêta : First, go into the building to get some water. Proceed through the level via the only routes possible. After you fill the Soaker with oil, you can jump off a ledge to return to where you started. Now, oil the rusted crank. Follow the newly raised path. When you get to the moving platforms, hop across the 3 rows of them to get to the other side, leading you towards the Zoni.