Sora, Donald, and Goofy return to Hollow Bastion, only to be greeted by a larger group of Heartless. As they ponder how the swarms have been getting bigger, a group of Nobodies pass by as well. Continuing on through the market, they discover Cloud, one their allies from Olympus Coliseum, standing there, pondering on his conflict with Sephiroth. Cloud warns the trio about Sephiroth, before moving on.
The trio get to Merlin's house, where Cid announces that Leon and Aerith have found Ansem's computer. Hopeful that the computer can give more details about Organization XIII, the trio rush off. On the way, they meet a trio of fairies named Yuna, Rikku, and Paine, who appear to be working for Maleficent, though Paine stops Rikku from revealing this.
Reaching the outsides of the castle, Sora finds Aerith, who reveals that King Mickey is with Leon. They hurry inside, but upon finding the lab, there was no signs of Leon, Mickey, or the computer. Just then, a woman budges in. She asks if the party has seen anyone with spiky hair. When Sora pulls on one of his own spikes, the woman laughs and replies "spiker", to which the trio deny. After a brief check throughout the room, she leaves while apologizing to the party for bothering them.
Moments later, Leon appears behind them, and reveals an open passage to the computer room. Turns out that he didn't want the woman, Tifa, to know about the computer in case she could damage it. As Sora tries to ask the computer on details of his missing friends, Leon cautions him on using the computer in a reckless matter. But just then, a small blue thing jumps onto the keyboard, promoting a furious Donald to leap at him. The creature escapes, and Donald turns around in anger...
a voice suddenly flares up, warning the four to stop using the computer, or else. Donald is still on the keyboard, and in trying to get off, he accidently steps on another key, to the chagrin of everyone else. The voice then announces that they're all under arrest, to Sora's surprise. As he and Goofy try to remove Donald from the computer, Leon notices a light coming from the large laser on the other side of the room, and warns them to flee. But it was too late, as Sora, Donald, and Goofy are zapped by the light and disappear.
Sora regains consciousness, but is stunned to see that he's wearing armor. But then he sees several Heartless leading Donald and Goofy away. As Sora tells them to "show em who's boss", their leader, Commander Sark, shows up, then tortures the two (or Sora himself in the manga adaptation) to show he's the boss.
Locked in a cell, the trio ask what sort of world did they end up in. A fellow cellmate then explains they're in the computer itself, and that the MCP has been running the system for some time now. The cellmate then introduces himself as Tron, a security program who was tossed into the slammers for opposing the MCP. He tells the party that the only way out is through a terminal. The bad news is that the MCP cut the power 50 microcycles ago. The good news is they can turn it back on from the inside. But the bad news is that they're still in jail. But then Sora reveals he's good news, too. He uses the Keyblade to break them all out. Impressed, Tron offers to help the trio escape.
They reach the core terminal in a junkyard, and repair it, allowing the trio to escape back to Hollow Bastion. In gratitude, they offer to help Tron in his conflict with the MCP by finding his user, and getting the password for the DTD if it means getting his full functions back, and hopefully get the goods on Organization XIII. But there's just one problem: Tron's user is Ansem the Wise. But before Sora could tell Tron that Ansem is dead, the MCP finds them, forcing them to leave right away, with them promising Tron that they're get the password.