Shortly after defeating Pandora and claiming the third and final Sacred Treasure, Sora, Kairi, Pit, Pikachu, and Angel have started to make their way towards the Palace in the Sky, so Sora has let out his Charizard and Dragonite as Pit has put his newfound ability to fly to the ultimate test.
"Wow, this is amazing!" Pit exclaimed.
"Don't pat yourself on the back yet, Pit. Some of our enemies will be coming right at us," Sora said.
"Pikachu," Pikachu said.
And he was right, because a couple of Gryphoons started to fly their way towards them. Pit used an Arrow of Light to destroy one of the griffon-like Heartless. Kairi threw her Keyblade at the other one, destroying it. Just then, five green idol-like creatures came down. They have yellow eyes, yellow lips. These are known as Totems. Pit fired at the Arrow of Light at the Totems as Charizard fired Flamethrower at them, turning them into charred dust. Just then, several pink starfish-like monsters came flying at them. They have blue bottoms and dagger-like teeth and green eyes. These creatures are known as Moilas. Dragonite unleashed Dragon Pulse and struck the Moilas on the mark. Charizard fired another Flamethrower and burned them up. Air Soldiers came flying at them, so Pikachu fired Thunderbolt at the flying Heartless, destroying them. Coming at them is a one-eyed monster wearing a blue robe with purple trimmings. It has three fingers on each hand and three toes on each foot. This creature is known as Erinus. Pit fired at the Erimus, but it comes apart, so the body parts go flying at them.
"Spread out!" Pit called out. They scatter as they the body parts go flying.
"Man, this is freaky," Sora said.
"Freaky is right!" A voice spoke. Thanatos appeared before them and he grinned evilly. "And this is as far you're gonna get."
"Who is this?" Sora asked.
"Thanatos. He's the God of Death. And he's Medusa's right-hand man," Pit said.
"You little kiddies have been very naughty for getting in the way and you need to be punished! Here I come!" Thanatos said as he came at them. He starts up by turning into a scorpion and attempts to sting them. Thanatos clamps his claws at them, but Sora smacked the pincer with his Keyblade and smacked him as Thanatos fired at Thanatos, making him change back. "Ooh, you little brat!" THanatos turned into a giant foot.
"A giant foot?" Kairi asked.
"What? Never heard of Athlete's Foot?" Thanatos asked as he stomped down, but Kairi smacked her Keyblade on Thanatos as she casts a thunder spell, shocking him. He changes back and then he turned into a bat and flew at them. Pit fired at Thanatos as Charizard fired Flamethrower at him. He gets hit hard by the flames as Sora and Pit smacked Thanatos on the mark.
"Got any other tricks for us?" Sora asked.
"Oh, I got all sorts of tricks up my sleeve, but I'm gonna use it since it has the right bite and it'll put the bite on you!" Thanatos said as he transformed into a giant snake. He hisses as he attempts to strike them, but they dodged. Sora swung his Keyblade, making Thanatos scream. "You will pay for that, you, little bratsss." Thanatos crawls and attempts to put the squeeze on Kairi, but she cartwheels out of the way and she casts a blizzard spell, freezing him in place. Pit lunged a blade into Thanatos, making him scream in pain. Thanatos attempts to strike at Pit as payback, but Sora casts a balloon spell, hitting Thanatos on the mark, and then Sora, Kairi, Pit, Pikachu, and Angel gave the God of Death one, last hit onto him.
"Crushing victory!" Pit said.
"Crushing defeat!" Thanatos said as he exploded in a burst of energy.
"Let's go! Medusa has to be inside!" Pit said.
With that said, Sora, Kairi, Pit, and the Pokémon continued on their way. As they went in further, a bunch of a ghostly figure wearing a white cloak with blue trimming. When active, it has fiery orange eyes, a pink face, and a gaping mouth with sharp teeth and a long tongue. It possesses two skeletal arms, and massive claws with red tips. This ghost is known is known as Zuree.
The Zurees slashed at them, so Sora and Kairi both casts a fire spell at them, engulfing them in flames.
Just then, Heartless, Totems, Moilas, and a couple kind of creatures came at them.
One of them appears as a small flower creature with orange petals on its head, two leaves for arms, and a pair of small legs. Though it initially seems to have a face with blank white eyes, its true face lies hidden within its petals, where it has black eyes attached to blue eyestalks, a gaping hole from which it spews its bombs from, and three blue tendrils underneath. This creature is known as Daphne.
Another are blue-skinned, humanoid creatures with talons for feet and wings for arms. They have fangs protruding from their mouths, long, purple hair styled in buns, a long tail feather, a brown skirt, and a breastplate to match. Theae creatures are known as Syrens.
The Daphnes fired flower bombs at them as the Syrens blew wind at them, but Sora casts a fire spell as Kairi casts a stone spell, hitting them on the mark. They get past the creatures as they eventually reached the throne room.
Laughter echoes through the throne room as she appeared before them.
"I have been waiting for you to come, Sora, Kairi, Pit. Ganondorf and Giovanni want you out of the way and I'm not letting you seal up the Keyhole!" Medusa said.
"We're not going to let you cover this world in darkness!" Sora said.
"And we're going to stop you in your tracks!" Kairi said.
"Pika!" Pikachu said.
"Eevee!" Angel said.
"Alright, prepare to die!" Medusa exclaimed as she grew to giant sized. She unleashed red and black orbs. Charizard and Dragonite flew to avoid Medusa's attack. Medusa unleashed a barrage of spells at them, so Pit blocked with the Mirror Shield as the Wings of Pegasus carried him. Medusa swings her staff at them, but Angel dashed at her with a Quick Attack and hits her on the mark. Pikachu unleashed an Electro Ball and lands a hit on her face.
"Got her!" Sora cheered.
"Think again!" Medusa said as she laughed as she attempts to slash at them and attempts to turn them to stone, but Pit came at Medusa and gave her a shot with an Arrow of Light and struck her hard. The fight went on between the forces of good and evil. Medusa's body then turned to stone and shattered, leaving only her head. "Now you've done it! Time to teach you some respect!" Medusa's head turned scaly and green with a large single red eye. The snakes all turned yellow. Medusa's snakes fired beams of energy from their mouths as Sora, Kairi, Pit, and the Pokémon avoids the beams. Dragonite rushed at her with a Dragon Pulse, landing a hit as Sora and Kairi smacked her with their Keyblades as Charizard gave her a Slash. Pit gave her one final blow, finishing her off.
Medusa screamed as her head dissolves into darkness and back to the Underworld. This triggers Palutena's release and she smiled. Sora, Kairi, Pit, Pikachu, Angel, Charizard, and Dragonite makes a landing after the fight.
"Well done, Pit. I knew you could do it," Palutena said, approaching them.
"Lady Palutena! I'm glad to see that you're alright," Pit said.
"Well, any later then I wouldn't be," Palutena said. She sets her attention to the couple and their partners. "And I would like to thank you for the assist, Sora, Kairi, Pikachu, and Angel. You saved our world and me as well, so I am grateful for what you did."
"We only did what was right," Kairi said.
"Vee," Angel said.
"Now we only need to seal the Keyhole," Sora said.
"I think I can help you out with that. Here," Palutena said, revealing the Keyhole. Sora points his Keyblade at the Keyhole and fired a beam of light from it. A locking sound is heard.
Meanwhile, over to Hollow Bastion, Ganondorf, Giovanni, Bowser, Dr. Eggman, King K. Rool, and a couple of villains watched the fight.
"Well, well, it looks like even the Goddess of Darkness couldn't cut it," Bowser said.
"Even a Goddess has a weakness. Apparently the children found the weakness and used it against her," Ganondorf said.
"They are becoming a problem. Those kids found another Keyhole and locked it up," King K. Rool said.
"Fear not, K. Rool, they will not find them all. And even if they do, it will be too late to stop us," Ganondorf said.
Back to the Palace in the Sky, Palutena stood before Pit as he kneeled to the Goddess of Light. All of the Centurions were freed from Medusa's spell and they dealt with the remains of the Underworld Army.
"Pit, you risked your life to save the world of humans and angels from eternal darkness and evil. All would have been lost if it weren't for your bravery and determination. So it is an honor to hereby name you as Captain of my Guard!" Palutena said. The Centurions all cheered. Pit smiled as he stood up.
"Thank you, Lady Palutena. I will do everything I can to uphold the principles what the title represents!" Pit said. Sora, Pikachu, and the Centurions all salute the newly appointed captain as Kairi and Angel giggled.
"Well, now that this world's safe, we should be on our way," Sora said.
"We're gonna miss you," Palutena said.
"You sure you gotta go?" Pit asked.
"Yeah, because we still have a mission to do," Kairi said.
"Yeah, you're right. I gotta take my new position seriously. One of my priorities is catching Pittoo since he got away," Pit said.
"Pittoo?" Sora asked.
"Well, that's what I decided to call him, I mean Dark Pit sounds dramatic," Pit said.
"That makes sense, I guess," Sora said. "Well, take care of yourself, Captain Pit."
"You too, Sora, Kairi," Pit said.
"Bye!" Kairi said.
Sora, Kairi, Pikachu, and Angel took their leave as they head for the Gummi Ship and depart for their next destination.