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'll get the password.
Back outside the computer, Sora, Donald, and Goofy discuss with Leon how they can get their hands on the password if the computer's User is no more. While searching the lab, Tifa moves the portrait of Ansem, revealing a sort of diagram behind the wall. They read the diagram and realize that the "DTD" Tron was talking about stands for "Door to Darkness," which is very fitting acronym for Ansem. While pondering over what the password could be, Mickey suddenly appears. He shushes them, telling them to keep their voices down because Organization XIII might be listening to them. Mickey recalls that the seven Princesses of Heart were needed to open the "DTD," so the names of the princesses must be the password.
Mickey says that he hopes they can use the data in the computer to find out where Ansem is, but Sora takes this as a joke. Mickey realizes that he has some things to explain, but before he can do so, Leon reminds them that Tron is waiting for them. Mickey assures them that he'll wait for them to come back, so they go back to the computer and reenter Space Paranoids.
Inside the computer, Goofy starts messing around, suddenly causing them to be transported to a "game grid." Sark tells them that they have to win the games or be derezzed, but he assures them that no one ever wins. Sora boards a light cycle and fights some Heartless as he drives through a maze. One of the Heartless blasts a big hole through the wall, so Sora makes his way to that wall and escapes through the hole. After making it back, they tell Tron that they came back to give them the password, but he asks them why they didn't just enter it into the computer from the real world.
They make their way to the dataspace, where Tron enters the names of the seven Princesses of Heart. While the DTD is being accessed, they are forced to play another "game," which is actually a security system. They deal with it, and the DTD is accessed, restoring all of Tron's original functions. The MCP speaks and reveals that letting them access the DTD was part of his plan, because it has now allowed him to seize full control of the system. The MCP finds a self-destruct program for Hollow Bastion, and he prepares to launch it. Tron changes the password to buy them some extra time. He tells the trio that the MCP uploaded a hostile program to the I/O tower. They need to go there and delete this program to stop the MCP from destroying the town.
After making their way to the I/O tower, the MCP asks Tron why he chose to ally himself with the Users. He says he has an unknown "command" within him that is urging him to help. Sora explains that the command is actually friendship. They fight the Hostile Program and successfully delete it. Tron tells them that he has a chance of fighting the MCP, saying that that is what Ansem would want him to do. Sora tells Tron that they found the password by accident, and that Ansem was actually their enemy. Tron surprises him by telling him that Ansem is actually his enemy as well, because he was the one who restored the MCP to the system. He tells Sora that there was once a time when Ansem would never do a thing like that, which confuses Sora even more. Before the trio leaves the computer, Tron tells them their names are now the new password. He wishes them well before sending them back to the real world. With the password now in their possession, Sora and friends are ready to learn what kind of knowledge Ansem truly possessed...
- Ability Required to Proceed: Defeating the Hostile Program will boost the Drive Gauge, which is required for the "Under the Sea" chapter in Atlantica.
- Arc Hero: Tron is the world's Guest-Star Party Member.
- Arc Villain: Ansem, Seeker of Darkness, in a posthumous way. The MCP takes advantage of Ansem's treachery and summons the Hostile Program to wreck the town.
- Death Course: Sark sends the party to the Game Grid when they return with the password. We don't see where Donald and Goofy are sent to, but Sora ends up in a game of Light Cycle, and escapes when a Heartless opens a hole in a wall.
- Fisher Kingdom: In Space Paranoids, the party is placed in armor with cyan circuitry. Sora, in particular, resembles a cyberpunk Knight in Shining Armor.
- Five-Second Foreshadowing: "The Ansem I first knew wouldn't do that." Almost right after accessing the DTD in Hollow Bastion around two minutes later, SDG learn that the Ansem they fought in the first game was actually Xehanort, Ansem's treacherous apprentice who stole his identity. And the current incarnation of Master Xehanort.
- Frame-Up: Played for laughs when it looks as though Goofy had accidently sent Sora and Donald into the Game Grid, before turning around, stating he didn't do it, and was captured himself. Turns out Goofy was framed by Sark.
- Inside a Computer System: Space Paranoids itself is a world within the computer of Ansem the Wise.
- Kick the Dog: Donald and Goofy are subjected to an Electric Torture in front of Sora, who surrenders to Sark to save them.
- Locking MacGyver in the Store Cupboard: All Tron needed in order to get out of jail was a Keyblade, and Sark decided to place Sora in the same cell as him. Sora befriends Tron, and helps him escape.
- Mythology Gag: The beam that strikes the party after the DTD is accessed works just like the lightning bolts in the Thunder Plains in Final Fantasy X.
- Prison Episode: The party is captured and thrown in jail because Donald tampered with the keyboard one too many times (by accident). Too bad for the MCP that they not only had a Keybearer in their group, but were placed in the same cell with an infamous renegade who joins them.
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Spiritual Successor: To Neverland from the first game. Both are the last Disney worlds visited, have much stronger ties to the overall story, and their episodes begin with the party captured by surprise and the Guest-Star Party Member helping them escape. Said guests become a Required Party Member for a certain battle* , but are not locked into the party. Also, Sora is forced to comply with the villain in both locations when an ally is taken hostage. - You All Meet in a Cell: Sora and his friends encounter Tron for the first time while they're all locked in a jail cell.
