After The Darkness was defeated by Wario, he met Blaire and made him his apprentice. Together they built the energy source, which was designed so that anyone in the confines would have their powers transferred to The Darkness. After the battles against Liquid Snake, Mr. L, the Darkness, and Ness sensed new adventure in the direction of the Energy Source, and suggested that he and Snake go check it out, thus beginning Operation: Blind Storm.
Ness and Snake were out looking for the adventure that Ness sensed. First, tey first find the Darkness' cap in the field where he was killed. Ness puts it on and learns of the Darkness' fail safe that he left behind in case he was killed: The Energy Source. He and Snake locate it in Bowser's hideout, but before Snake can destroy it, Mario, and Luigi, and Wario stop him. Wario had spoken to Merlin earlier, who had told Wario not to let them destroy it. Both Ness and Wario make logical reasoning to prove their respective points, but Snake ends up destroying the Energy Source with his gun.
Ness collapses on the ground and Shadow Mario's voice is heard. He tells them that the energy source was a beacon which allowed them to use their powers in the Real World. The heroes regain consciousness the next day and find that their powers are truly gone. However, Mario sees the good side of this; now they can live completely normal lives like they intended to, seeing as any villain that comes to the real world will be powerless as well. Ash then arrives, complaining that his Pokéballs don't work anymore, but Luigi reminds him that they never worked anyway. Wario finds that his Fireballs don't work. Ash then exclaims that his Pokemon games don't work, but there wasn't a cartridge in the Game Boy. He puts one in and exclaims that the powers are back, then gets hit by his Pokéball.
Months after Operation: Blind Storm, Solid Snake comes to Mario, claiming he saw Liquid alive and well. He demands that they try to get the powers back. When Mario points out that the Energy Source was destroyed, Snake counters with how easily it was to destroy it with one human bullet, which he finds unlikely. Later, Wario also demands that they get their powers back. In the episode "Poke-Suckers!", it is revealed that Waluigi can still throw fireballs. They later get their powers back due to Waluigi transferring his powers to Mario, Luigi, Ness, and his best friend Wario before falling into a coma for an unknown amount of time until they recharge.
In "The Darkness Explains It All," the Darkness reveals the true purpose of the Energy Source. It was a "power transfer compulsion system" created by himself and Blaire Vherestorm. Once it was destroyed, it absorbed the powers of everyone within the confines of the cave and transferred them to the Darkness, allowing him to gain four times Nox Decious' power and become the most powerful being in existence. Even with this power, he couldn't regenerate until the heroes had their powers back.
- The destruction of the Energy Source most likely doesn't affect Ash, Brock, Gary, Professor Oak, Otacon, or Snake, seeing as they didn't have powers to begin with.
- The destruction of the Energy Source prevents Pokémon from coming out their Pokéballs, although they didn't even work anyway.
- It may be based off of the Beacon from the game Super Mario Galaxy, which is a huge ball of energy that grows when the players progress more in the game. One of its colors is light blue like the one in Stupid Mario Brothers.