During this last period, the player will play as Aqua, effectively now the only one remaining of the three protagonists. Upon completion of this Final Episode, the player will be able to activate the Vanitas Remnant and Young Xehanort battles. The Final Episode is unlocked after finding all the Xehanort Reports and completing each of the three characters' storylines.
Aqua carries Ventus out of the Mysterious Tower; as she realizes she doesn't know where to go, Ventus summons his Keyblade and opens a door to the Land of Departure. Once there, Aqua sees her home's ruined state for the first time and is horrified by it. She finds her Master's Keyblade, picking it up, and goes inside.
She places Ventus's body in the central throne and recalls what Master Eraqus said to her after she became a Master; using his Keyblade, she locates the Keyhole behind the throne and locks it. When the resulting flash of light fades, Aqua finds herself in the Chamber of Waking, with Ven still in the chair in the middle of the chamber. She promises Ven that she will come back after she finds Terra.
Going outside, she looks back at the castle, now transformed into Castle Oblivion. She then hears Terra's voice, asking her to "put an end to me", and she departs to find him, following his voice to Radiant Garden.
There, she finds the amnesiac Xehanort, whom she believes to be Terra. After a brief hesitation, Xehanort grabs Aqua by the chest and bodily lifts her off the ground with one hand while inquiring his identity. Sensing the powerful darkness inside him, Aqua pleads for Terra to fight it, but instead, Master Xehanort regains control of the body, and proceeds to try and eliminate Aqua.
After battling both Xehanort and his guardian, Terra begins to retake control of his body, but Master Xehanort fights back, resulting in Master Xehanort using his Keyblade in an attempt to release Terra's heart from within him, but this results in Xehanort and the guardian being dragged into the Realm of Darkness. Aqua jumps in after them to save Terra.
Aqua manages to retrieve Terra's body, and tries to head back towards the Realm of Light. However, it soon becomes clear that Aqua is not able to save the both of them, so Aqua sacrifices herself, her Keyblade and armor so that Terra can make it back, stranding herself in the Realm of Darkness as she apologizes to Ven for being later to return to him than she thought.
Meanwhile, on Destiny Islands, Sora and Riku are lying on the beach of the main island. Riku decides to go home, and Sora agrees. While they walk home, Riku notices a tear rolling down Sora's cheek, which neither understand. Riku suggests it's because somebody under the same sky as them is sad, and that maybe Sora should call out to them with his heart. Sora doesn't truly understand, but decides to give it a try. Ven is shown in his resting place, with Sora's voice asking if he can hear him.
Back in Radiant Garden, Braig leads Ansem the Wise and Dilan to the spot where Xehanort and Aqua's Keyblade and armor lie. Ansem questions the young man, who has complete amnesia. The young man reveals his name to be Xehanort, to which Braig gives a triumphant smile. Xehanort then falls unconscious; Ansem has Braig carry Xehanort back to the castle. Braig asks Dilan to retrieve the Keyblade and armor.
Some time later, Aqua wanders throughout the Realm of Darkness. A Darkside rises before her, and she summons Eraqus's Keyblade and prepares to fight. Suddenly, three more Darksides appear, and Aqua contemplates simply giving in to the darkness, dismissing the Keyblade. Before one of the Darksides has a chance to strike, two beams of light appear and vanquish the Darkside pack; upon closer inspection, they are revealed as the Earth Shaker and the Wayward Wind. Aqua then smiles, something she realizes she had almost forgotten to do. She takes her Wayfinder out of her pocket, and proclaims that there is always a way.
Sora appears on a Dive to the Heart Station. Looking up, he spots Ven's heart floating down above him, and asks it if it can hear him. It does, saying he followed it to a sea of light, as it lands in Sora's outstretched hands.
Sora asks if the heart is sad, as it asks Sora if he can join with his heart once more. Sora agrees, saying if it makes him feel better. Ven thanks Sora, and rests within Sora's heart. Back on the beach, Riku asks Sora if it worked, and Sora says that it did.
The Final Episode, as well as Kingdom Hearts Birth by Sleep, then closes with the caption: "In time, the worlds would be saved by these two heroes who stood beneath the same blaze of stars."