The tower's location was only truly seen in the universe of Kingdom Hearts. The tower is located on a floating isle while the isle itself is surrounded by hilltops and empty space. On the isle resides wildlife and the tower itself.
In the original film where the tower makes it's debut, only the interior of the tower is shown. In the tower lives Yen Sid and young student Mickey Mouse. When using Yen Sid's sorcerer hat, the now Sorcerer Mickey creates a flood and the tower is filled with water. The tower is soon cleared by Yen Sid.
During Kingdom Hearts Birth by Sleep, Mysterious Tower is first seen at the beginning of the game. Mickey is shown riding a book over waves of water, before being sucked down a whirlpool. Suddenly, the water disappears and Mickey appears in Yen Sid's study. Yen Sid looks disappointed, before saying that he senses that something horrible is about to transpire.
Terra is the first of three Keyblade wielders to visit the tower. After learning that Master Xehanort is in a battlefield wasteland from the Magic Mirror, Terra goes to see the former Keyblade Master, Yen Sid to gain more information. As he arrives, he sees Mickey disappear into a flash of light from his Star Shard. Terra continues to go see Yen Sid. Yen Sid sensed Terra's arrival and Mickey's departure as he can sense the movements of Keyblade wielders. Yen Sid says he feels that the Unversed and Xehanort may be connected and sends Terra back on his search for Xehanort. As the young man leaves, Yen Sid asks himself if Xehanort still has "distracting thoughts".
Ven appears here accidentally by Star Fragment while visiting Neverland. As he lands, Donald and Goofy are sitting outside wondering where their King has gone. They at first mistake Ven for the king but then take him upstairs to Yen Sid. The old man notes that Eraqus ordered Ven to return home, but says Ven is just like Mickey that way. Ven says that he does not know where Mickey is, so Yen Sid finds him. He shows Ven, Donald, and Goofy an unconscious Mickey in the Keyblade Graveyard, abducted by Master Xehanort. Donald and Goofy prepare to venture out to save Mickey, but Yen Sid persuades them otherwise, knowing that they are no match for Master Xehanort. In the end, Ven goes alone, to repay his debt to Mickey for saving him earlier.
Aqua comes here after finding Mickey unconscious in the space between worlds. She flies him to Yen Sid, and while Donald and Goofy try to wake him up, Yen Sid tells Aqua of Eraqus' defeat at the hands of Terra. Aqua furiously denies that Terra could do that. Yen Sid hopes this as well, but tells Aqua to find the truth by talking to Terra himself in the Keyblade Graveyard. She leaves with Yen Sid warning her to be careful. After Aqua's showdown with the Vanitas-possessed Ventus, Mickey brings the two to the Mysterious Tower.
However, Ven is unconscious, stuck on the border between light and darkness. Yen Sid tells Aqua that she must believe in her friends to save them. If she treasures the bonds she shares with Ven, he will be led back to light. Mickey agrees to believe in Ven too, and Aqua says Terra will too, when she finds him again. Until then, Aqua departs with Ven to find a safe place for him to sleep.
During the end credits, a dejected looking Mickey, standing beside Donald and Goofy, places his Star Shard and Keyblade on Yen Sid's desk. As he turns away, Yen Sid returns it to him, as the King raises it in pride.
After Sora awakens from his year-long sleep in the basement of the Old Mansion, he meets briefly with King Mickey, who gives him munny and tells him to take the mysterious train to Yen Sid. After being seen off by Hayner, Pence, and Olette, the three take the train and arrive at the base of the tower.
Getting off the train, the trio meet Pete, who is loitering outside after sending in Heartless to attack the Tower's master. Due to the tower having changed it's location since the events of Kingdom Hearts Birth by Sleep, Donald and Goofy are unfamiliar with the tower and are startled to hear that Yen Sid resides there. The three hurry inside to meet the King's tutor, leaving a bewildered Pete behind. They make their way to the top, slaying Heartless on their way up, and eventually reach Yen Sid. The sorcerer gives them a book that summarizes all three games, and gives them information about the Nobodies and Organization XIII. He and the good fairies also give Sora his new outfit and drive form abilities, and returns the lost Gummi Ship to Donald and Goofy.
After the party leaves, Diablo, Maleficent's Raven, arrives with Maleficent's robe that was left in Hollow Bastion. The three good fairies recognize it immediately, and their memories of its owner start to work magic on it and bring Maleficent back to life. She plotted to take over the Tower and announced her return with her trademark laugh.
It appears, though, that she failed, as she instead began targeting other castles all over for the same reason, and later, when the player can return to the Tower, there is no evidence that she ever held any sway over it. However, Yen Sid and the Good Fairies are completely absent, and the Tower is overrun by lesser Nobodies.
Some time after decoding Jiminy's Journal, Mickey returns to the Mysterious Tower to meet with Yen Sid, who appears to have regained control of the Tower from the Nobodies. They discuss the whereabouts of Terra, Aqua and Ven, as well as the next actions of Master Xehanort, who will be revived due to the defeat of Ansem and Xemnas. Yen Sid orders Mickey to summon Sora and Riku to him to undertake a Mark of Mastery Exam to counter Master Xehanort.
The tower was accessed by Mickey Mouse via mirror located inside his own bedroom. Inside the tower Yen Sid was creating a world for forgotten and rejected Disney characters. Mickey sneaks in and accidentally creates a monster and rushes out. He was later taken back into the tower and inside the ravished world. Near the end with the world saved he exits the world and forced out the tower by Yen Sid.
- In an Disney Magix cereal promo, the tower's exterior was actually seen for the first time. It was a castle and more or less resembled it's appearance in Kingdom Hearts. In front of the castle was a bridge crossing over to a forest.