Energy Breaker is set on a small, fictitious island called Zamlia. There are a few hints that Zamlia exists on the world that the Lufia series takes place in; namely, the presence of Priphea flowers, some terminology and conventions, an obtainable sword named after the Dual Blade, and a cameo by Lufia and Roman in the ending.
The story begins with Myra, a 21-year-old girl who has lost her memory. She keeps having dreams warning that she must hurry to avert a catastrophe. After visiting Selphia, a fortune-teller who has just come to the town Myra lives in, Myra gets a lead on her identity when she is told to seek out a man called Leon, the “Whirlwind General” in a nearby forest cave known as the Eltois Forest. She is then gifted a jewel called the Emerald of Light. While looking for Leon, she runs into a local scientist and inventor, Lenardo, and his robot assistant Gulliver. She then comes to join him on his adventure to find a flower called the Reincarnation that can bring the dead back to life.
After their adventures in Eltois, Selphia gives Lenardo another jewel: the Sapphire of Light. As Myra and Lenardo travel on, they cross paths with foes such as Parasite, the General of Hellfire and Limitz, the Twilight General, who are on a mission to capture the jewels given to them by Selphia…