After having searched wide and far, Sora, Donald, and Goofy haven't been able to find out how to get into Organization XIII's stronghold, so they return to Hollow Bastion, only to find it under attack once again by huge hordes of Heartless. This time, though, the Heartless are different; they're the same ones from Space Paranoids, the world inside Ansem the Wise's computer! What's more, the security system has turned against them, and now it is helping the Heartless. The trio heads for Merlin's house, where they learn that the MCP has started going haywire again. Leon went to Ansem's lab, only to find that the MCP has been generating Heartless with the machine that Xehanort originally used to create them. Cid tells them that he's making an MCP Eradication Program, but it will be a while before it's ready.
The trio fights their way through Hollow Bastion, dealing with the MCP-spawned Heartless along the way. After reaching the castle, they meet Yuna, Rikku, and Paine again. They found out that Leon didn't actually have any treasure, but they decide to forgive them, and they even give Sora a new Keyblade chain as thanks.
Leon and Aerith are waiting for them in Ansem's computer room. Leon asks them to go back into the computer to find Tron and to head to the I/O tower, where they'll upload the program to eradicate the MCP. He heads back to Merlin's house t check on its progress. While they enter the game grid, Cid manages to complete the program. Sora and friends arrive just in time to help Tron deal with some Heartless. After making it back, they explain about Cid's program. Leon hurriedly takes it back to Ansem's computer room while Sora and Tron fight their way to the I/O tower.
Aerith loads the program, which gives some extra powers to Tron, including giving him access to the solar sailer. They go there and fend off Heartless while it takes them to the MCP. Once there, he sics Commander Sark on them. They seemingly defeat Sark, and the MCP tries to persuade Tron to join him. When he refuses, the MCP gives Sark a power boost that makes him grow. They manage to defeat the newly-empowered Sark and the MCP itself. With the main program controlling the computer gone, it now needs a new main program. Tron decides to take the MCP's place and becomes the controller of the system.
Back outside, they learn that the extra Heartless spawned by the MCP are no more, and the security system is back to normal. Tron, now in control of the computer, shows them an image of Hollow Bastion from its glory days. Seeing it causes Leon and friends to recall the world's original name: Radiant Garden. The world became known as Hollow Bastion once Xehanort ruined it and Maleficent took over. Now that the Restoration Committee has largely managed to restore it to a proper town, they decide to officially change its name back to Radiant Garden.
After dealing with the MCP, Sora and friends head back to the bottom of the canyon where they met Xemnas. Once there, they see Sephiroth. He tries to ask them where Cloud is, but Sora doesn't know. Sephiroth takes interest in the Keyblade, so he attacks Sora in the hopes of taking it for himself. In a fierce duel, Sora manages to hold his own and seemingly triumph, but Sephiroth doesn't even have a scratch on him. He says that only Cloud can destroy him, so he asks Sora to go find him so they can settle their rivalry once and for all.
Sora finds Cloud in the town and tells him about Sephiroth. He heads down the canyon, and they have a climactic duel. During the battle, Tifa finally manages to find Cloud, who says that she is his light. Cloud and Sephiroth fly up into the sky and vanish, leaving Tifa to start searching for him all over again.
Before leaving Radiant Garden, Sora remembers that a strange cave opened up near the castle. They ignored it previously due to the ongoing battle, but now he decides to investigate. The cave, known as the Cavern of Remembrance, contains the toughest Heartless and Nobodies they've fought, but they manage to make it through to the end. They find a place called the Garden of Assemblage, which contains data based on all the members of Organization XIII. Sora manages to triumph over them and gets rewarded for his efforts. With that, they move on, nearing the end of the journey...
- Ability Required to Proceed: To unlock the Goddess of Fate Cup, you need to defeat the Master Control Program.
- Arc Villain Duumvirate: Sark and the Master Control Program.
- Breather Episode: This is the last episode set before the Storming of the Castle That Never Was, and serves to tie up loose ends with the Hollow Bastion Restoration Committee and Tron.
- Call-Back: To Atlantica; Sora suggests he and his friends should tamper with Tron's source code to get him to sing and dance.
- Close on Title: Like most worlds, Hollow Bastion's title card appears again upon the episode's conclusion. Only this time, the title card updates itself so it now reads Radiant Garden.
- Disney Death: Tron intentionally jumps into where the MCP once stood, to the horror of SDG. As they returned and mourned his apparent death, Tron reveals himself to be alive, and that his actions were just to retake the computer system from Organization XIII's control. Returning afterwards shows he's still in the party.
- Earn Your Happy Ending: The MCP is overthrown by Tron, and Ansem's computer is now safely in the hands of the Hollow Bastion Restoration Committee and Zexion. The town is fully restored to its former glory, and its original name: Radiant Garden.
- Elevator Action Sequence: A more horizonal case is the Solar Sailer battle that takes the party to the MCP's central core. It plays similar to the battles in Devil May Cry 3: Dante's Awakening, where the party has to defeat Heartless quickly due to a weight limit, or fail and start over.
- Foreshadowing: Tron spends most of the game as The Stoic, but after the MCP is defeated, he's just as joyful as Sora. Kingdom Hearts 3D [Dream Drop Distance] reveals Tron didn't have a heart, making him similar to a Nobody, but grew one of his own through his friendship with Sora, explaining his change in emotion. The same game also confirms Nobodies and other constructs like Puppets, Programs, and Replicas can also grow their own hearts through friendship.
- I Take Offense to That Last One: Cid calls Merlin an "old loon". Merlin retaliates by setting Cid's computer on fire.
- Not Me This Time: Sora thinks Organization XIII is responsible for the Claymores going rouge. It's only when he's greeted by Heartless normally exclusive to Space Paranoids does he realize that the real culprit is the MCP.
- Recruitment by Rescue: Since Tron has been tossed into the game grid, you need to clear it before he rejoins the party.
- Required Party Member: Double-subverted. Unlike "Ping", Auron, Jack Sparrow, and Simba in earlier episodes, Tron is not locked into the party when he rejoins, but he's needed for the MCP battle to use the "Delete" reaction command.
- Wham Line: "IGNORANT USER. OBEY THE MCP"
- Also, at the very end of the episode when Tron reveals to SDG and the HBRC the original town.
Aerith: You know, this town had another name once: Radiant Garden.
