Where the Fuel Cells are at in Metroid Prime 3

Energy Cell 1: Lying on the ground by the ship that's crashed on the Valhalla's docking bay. Just walk over it to pick it up.

Energy Cell 2: Obtained automatically when you first load up your ship with missiles on Bryyo. Apparently impossible not to obtain.

Energy Cell 3: Generator B, Norion. This one will require you to have progressed at least up to where you've obtained the Seeker Missiles. Use the plasma beam to fuse together the circuit board in the cargo hub, then head down to the Cargo Dock B. Destroy the Hopping Metroids there with cold missiles and your beam fire, then use seeker missiles on the door that's revealed. Head through to defeat the Metroid Hatcher, which you may have already seen on the Pirate Homeworld. If you haven't, then the process involves shooting the ends of the tentacles, then shooting the mouth before it can spit out metroids, then grappling the tentacles and pulling them away from the body. When the Hatcher is dead, roll through the ball tube to nab the energy cell.

Energy Cell 4: Hidden Court, Bryyo. In order to obtain this energy cell, you have to have extended the bridge in the Machineworks Bridge section of the area that connects the Thorn Jungle to the Federation Hangar Bay areas. To do so, first you need to use your Ship Grapple to grab the head of the statue in the Fuel Gel Pool and drop it on the statue in the Colossus Vista area. That'll open one side of the bridge area; use your boost ball in the spinner to extend that side of the bridge.

Next, land your ship at the Thorn Jungle landing side and head to the North Jungle Court, where you can use your Ship Grapple on a large structure in one of the alcoves. Do so, then follow the path that's revealed under it to reach the other side of the bridge. Extend it and walk back across. Head through the Hall of the Golems and get to the Hidden Court. Drop the battery onto the fuel gel pump here to extend the energy cell. Jump to the top of the room and use the halfpipe to access the energy cell.

Energy Cell 5: Connected to research station in Skytown Xenoresearch system. Required to get the Swarm Missiles.

Energy Cell 6: Command Courtyard, Pirate Command. Required to move on.

Energy Cell 7: Metroid Processing, Pirate Homeworld. Optional, but easy to spot under the floor when you charge up the core generator.

Energy Cell 8: Ballista Storage, Elysia. Where you originally found the boost ball. Drop down, defeat the Steamlord, charge the turbines, and remove the Energy Cell. Requires Energy Grapple.

Energy Cell 9: Phazon Quarry, Pirate Homeworld. After obtaining the Nova Beam, unlock the phazite door in the Main Cavern and follow it through to Drill Site 2. Use x-ray vision and blast the drill's interior red ball, then head back to the quarry and find the energy cell.