Chowder rescues many fighters and spirits (with Mayor always being the first fighter rescued) and defeats Mucho Eduardo (Giga Bowser), Galleom and Rathalos powering Galeem's shield. A Master Hand puppet appears to intercept but is destroyed. The fighters eventually defeat Galeem, but this victory is short-lived as a crack appears in the sky. The crack shatters and Dharkon and his army of Crazy Hands emerge, taking advantage of the situation and forcing Galeem to retreat. The World of Light is then swallowed by darkness with Dharkon taking control of Galeem's remaining spirits and fighters. The fighters continue to free the puppets and spirits under Dharkon's control, and defeat Uncle Grandpa’s (Ganondorf) beast form, Marx (in the art style of Invader Zim) and Dracula (Hotel Transylvania) to force Dharkon to appear. After the fighters defeat Dharkon he retreats but Galeem soon comes back and launches an assault with a new army of spirits and puppet fighters. Both of them try to defeat the other, but Mayor (Mario), Valhallen (Simon Belmont), Clarence, PB, Chowder, Rigby, Lapis, Eduardo, Blossom, Gumball and the rest of the fighters soon catch up in the middle with both Dharkon and Galeem noticing. The final battle is about to begin.

The fighters rescue Scotsman (Roy) and the Amoeba Boys (Dark Samus) and defeat a Master Hand and a Crazy Hand. Galeem calls on Melanie and the original Master Hand as reinforcements, while Dharkon calls on Him and the original Crazy Hand. The fighters also free all four from Galeem and Dharkon's control. this point, the Hands appear at the top center of the map, but there is no path to reach them unless the number of dark and light spirits on each side is equal or nearly equal. Once this condition is met, interacting with the Hands causes them to come to the fighters' aid which creates a fissure in the background where Master Hand dives in. He becomes a temporarily playable character as he defeats an onslaught of 50 puppet fighters consisting of Mayor, Finn (Link), Blossom, Mandy (Meta Knight) Hoss, Gumball, Mr. Small (Cloud) and Gus (King K. Rool), destroying the former light and dark background and replacing it with a golden backdrop. This opens up the paths to fight Galeem or Dharkon solo but the process also creates a new path in the middle where Galeem and Dharkon come together from their previous positions, face to face, for the final confrontation which leads to the true ending.

The fighters climb the long stairwell while being attacked by Galeem and Dharkon and defeating more puppets. Afterward, they fight all six bosses once again. The two deity-like beings continue to battle each other before turning their attention to the fighters in a three-way climactic clash. Even in the midst of a shared enemy, the two deities still wage war against one another. When both Galeem and Dharkon are destroyed, their armies vanish as they fall into the ocean and explode, cleansing the universe of their influence. Now free, the spirits return to their original worlds.