Sora, Donald & Goofy wake up one year later after Chain of Memories (three after the first instalment) in another world called Twilight Town where he gets a mission from Yen-sid to wipe out the heartless. Yen-sid also informs them about new foes to beware of, such as Nobodies and the evil Organization XIII. Sora quickly moves back to Hollow Bastion knowing that the evil Malifient is still alive and has Pete doing her dirty work, including to bug Sora every now and then. When at Hollow Bastion Sora goes and sees if he can find more information from his old friends Leon, Yuffie, Aerith, Cid and Merlin. Cloud has also joined in to help fight the darkness with a mission of his own on finding his heartless Sephiroth. Sora also decides while trying to take these foes down he needs to find Riku and King Mickey. All of the worlds have been restored thanks to Sora, Donald & Goofy, they now use the power of the keyblade to unlock paths to new worlds, becuse like hearts worlds are connected to one another by invivble binds.
The first world they visit to is the Land of Dragons, Where they find their old summoning friend Mushu and accompaning Mushu was a man named Ping. But Goofy soon figures out that Ping was acctually a woman named Mulan who was entering the Chinese army to honor and protect her father. Sora, Donald & Goofy promised to keep Mulan's secret from the other soldiers. Every time Sora runs into a member they refer to him as Roxas. Sora has no idea that Roxas is closer than he thinks. At the army camp Sora trains along with Mulan under orders of Captain Shang, who Mulan began to fall for. But while traing Sora and his freinds met an unlikely enemy named Shan-Yu who wanted to bring harm onto the Emporer of China and the Imperial City so he can rule it himself. Mulan is caught in her lie by Shang, who turns her away. But that doesn't stop her from protecting China. Sora helps along stoping Shan-Yu and saving China.
At their next stop (Beast's Castle), Sora Donald & Goofy run into their old freind Beast, who is acting very strange. Instead of greeting Sora and the others he just pushes them aside. Mrs. Potts, Lumiere and Cogsworth are worried too because he has Belle locked away in her room. When Sora reaches Belle she turns out to be just fine, but she asks him to go and help Beast. The reason Beast was acting so peculiar, was because he had a member of the Organization whispering in his ear telling him lies. Sora decided Beast needed some sence knocked into him. Beast begins to see straight and goes with Sora to apologize to Belle, but when they reach her room she is gone. They hear Belle crying out for help in the Ball Room. Beast and Sora hurry and when Belle runs out of the room they fight off the heartless that took her. Beast apologizes to Belle and thanks Sora for all the help.
Sora and the gang take the Gummi ship to Olympus Coliseum expecting to find Hercules, but much to their surprise they hear a woman screaming and they end up in Hades' territory. They help her out and she introduces herself as Meg. They decide they should see what Hades is up to and see him with a man who he raised from the dead. Hades asks the man named Auron to fight Hercules to the death. Auron defies Hades and Sora decides to help Auron escape, but Hades doesn't make it easy when he sends his hell hound Cerberus after them. Sora and Auron fight off the Cerberus and run into a member of Organization XIII named Demyx who has water forms attack. He soon escapes the Underworld and if things couldn't get any worse Meg is captured by Pete. Sora save Meg from Pete, but suspects that Pete will be back to bug him again soon. Sora goes up to the coliseum and sees that a Hydra has destroyed it. Sora, Donald & Goofy defeat the Hydra and see that Hercules is having probelms with his God like strength. Sora promises to return soon and headed off to the next world.
The Gummi ship is abruptly summoned to Disney Castle, where they see it is covered with heartless, which never happens. Sora, Donald and Goofy hurry to find Queen Minnie Mouse. She tells them that Cornerstone of Light is in danger, which is bad because it protects Disney Castle form being completly engulfed in darkness. So while Donald and Goofy storm the castle, Sora escorts Queen Minnie to it while protecting her from heartless. Queen Minnie has Sora get Merlin from Hollow Bastion to discover what is wrong. Merlin discovers that someone must have tempered with the past bt messing with the Cornerstone of light. Merlin creates a door for Sora, Donald & Goofy to go into the past.
While in the past atTimeless River Sora, Donald & Goofy run into Pete and fight him. When Pete doesn't fight back they find out it isn't the Pete that has been giving them all this trouble and that it's just Pete from the past. They later learn that the "real" Pete has been tinkering with the past and had help from Maleficent. They've been setting heartless on the construction of Disney Castle and in many other spots. But more havoc reigns when the the present Pete tries to steal the Cornerstone of light. After Sora stops him, the two Petes bump into each other. Sora fights off Pete and sends him out of the past and puts the Cornerstone into its original place. Once back into the present Sora, Donald & Goofy see all is well with Disney Castle. But before goinf Sora asks Queen Minnie if she knew where King Mickey or Riku was. She had to give them a dissapointing no.