Terra is the first person to appear in this world. After fighting a swarm of Unversed in space, he is swept on-board the Federation ship. He is placed, unconscious, in a prison cell and is visited by Captain Gantu and the Grand Councilwoman. He wakes up to a swarm of Unversed attacking the prison, breaks free, and fights the Unversed. He meets Dr. Jumba Jookiba who convinces him to unlock his cell so they can find Experiment 626, who is imprisoned somewhere on the ship.
When they find him and release him, Experiment 626 snatches Terra's Wayfinder. When Terra refers to it as his bond with his friends, Experiment 626 drops it and runs, to Jumba's surprise. To demonstrate that his experiments do not have hearts, Jumba activates Experiment 221 to fight Terra. After the fight, Experiment 221 becomes deactivated and Experiment 626 returns. Terra talks to Experiment 626 about friendship before alarms go off. Experiment 626 and Jumba run off while Terra leaves the world.
Aqua is the second person to arrive in this world. After fighting a group of Unversed as soon as she boards the ship, she meets Experiment 626, who runs off. She then meets Gantu, who brings her before the Grand Councilwoman, who charges Aqua with destroying the Unversed on the ship and locating Jumba and Experiment 626. Aqua soon finds Experiment 626 and fights Unversed alongside him. Experiment 626 runs off again, and the Grand Councilwoman directs Aqua to the departure bays to capture Jumba and Experiment 626.
When she finds them, she learns that Experiment 626 made a Wayfinder of his own. Gantu appears and attempts to destroy the three of them. Aqua and Experiment 626 fight Gantu for their freedom. After their victory, the Grand Councilwoman thanks Aqua for a job well done, and demotes Gantu. As she escorts Experiment 626 and Jumba away, Aqua then asks her to consider sparing Experiment 626's life. Before leaving, Aqua asks Experiment 626 to add her and her friends to his "bond".
Ventus is the last person here. He arrives on the ship after chasing a giant Unversed. He is confronted by Gantu, who runs off when the Unversed attacks the ship's engines. Ventus then meets an escaped Experiment 626 and learns that he has met Terra and Aqua, then see's Stitch's "Friend Circle". He then leaves Experiment 626 and tells him to stay, not wanting him to get hurt, and not know how capable he really is. Some time after that, Gantu finds Experiment 626 and destroys his Wayfinder, saying that Experiment 626 is nothing but a weapon of mass destruction. When Ventus finds the Unversed, Experiment 626 joins him in fighting it off. However, even after the battle, Experiment 626 is still agitated. He soon calms down and shows Ventus his ruined Wayfinder, who tells him that friendship is more than an object. Just after that, Gantu finds them and plans to arrest Ventus with Experiment 626, but they escape the ship, Experiment 626 in a red cruiser and Ventus on his Keyblade Glider. Experiment 626 accidentally activates his craft's hyperdrive, and Ven is blasted off by the cruiser's resulting pulses as Experiment 626 disappears into space.
In the ending credits, Experiment 626 has repaired his Wayfinder, which had been destroyed by Gantu, and puts it on the steering wheel as he flies off through space.
- Wonderland, Halloween Town, and Deep Space are the only Disney-based worlds that are not set on some version of Earth.
- Although the primary setting of Lilo & Stitch, Hawaii, appears in Stitch's summon sequence in Kingdom Hearts II, Deep Space is the only Disney-based world that is not based on the main setting of its film.
- Pleakley from the original Lilo & Stitch movie was set to make an appearance in Deep Space, but was removed for unknown reasons. His model is still in the game data, albeit without textures.
- Deep Space is the first Disney world in the Kingdom Hearts series to feature all of its home characters portrayed by their original actors from their original appearance in the movie. The minor exception to this is the voice of three "voice only" characters: The Ship's System, voiced by Stephen Stanton, the Patrol Officer, voiced by Andre Sogliuzzo, and the Cruiser Operator, voiced by Gina Tuttle.