After defeating Phantom and saving the factory, return to the factory to get a large number of Energy Crystals, especially in the last room of the level. Note: You can only get them once.
This trick requires patience and batteries. After completing the Reploid Disposal mission, go back to the area where the smashed truck is located. The truck has a Large Energy Crystal on it. When you get there, a Drop Reploid carrying a Spike Bot will appear. Slice, spear, throw, or blast them both and they may drop Energy Crystals (large or small). If you repeat this, you can feed and use your Baby Fairies. Metals will also drop -- if you have a Sub Tank you can fill it up. This takes hours but you will get to use those Baby Fairies that take two feedings.
This strategy may take some time. After defeating the truck in the disposal center, take the transporter back there. Run down to the set of ladders you see after the spike traps and the two pillars. Climb the ladders to the top where you will see a Carrier Bot holding a Spike Bot on the right. Destroy both of them, then another set should appear from the left. Destroy them, then continually run back and forth to respawn these enemies. If you continually defeat these enemies, they should drop Energy Crystals, Mettalls, and extra lives. Repeat this to feed your elves and also get the maximum 9 lives.