From Olympus, Pete is replaced by Robotnik. This was so Robotnik could pull an Eviler than Thou to Hades.
From Halloween Town, Jack's past attempt to host Christmas.
Any Ship Tease between Roxas and Namine, due to Emerl enforcing Spared By Adaptation onto Xion. For the same reason, Roxas is unable to dual-wield.
Dies Differently in Adaptation: Xion doesn't die from her Suicide by Cop attempt, as Emerl stops it. Instead, she and Roxas are brought by Emerl to Mobius, where Dr. Koopa (against Emerl's wishes) puts them into the same Lotus-Eater Machine until he finds a way to stabilize Xion. However, his plans are derailed by DiZ, who brought Sora's capsule to Mobius and awakes them from it, forcing them to return to Sora. At least this time, Roxas did not forget Xion. Needless to say, Emerl hated it.
Even Evil Has Standards: With all his desire to unleash the Titans and take over Olympus, Hades did not want Chronos to have Any part in his plans, as Metallix state that Chronos wants to kill all gods and destroy Olympus, not help one of the gods to take over Olympus.
Eviler than Thou: Robotnik pulls one to Hades by unleashing Chronos behind his back. For all his desire to take over Olympus, Hades didn't want to unleash his purely evil father.
Wham Episode: Emerl's repeated fight with Sora in The World That Never Was, particularly Sora's dialogul with Metallix in the Null Space, after Sora's 20th Defeat at Emerl's hands. Metallix basically reveals that Sora has been always bottling Up darkness in his heart; then, using a Time Stone, he reveals that, if Sora keeps bottling up darkness, Xehanort will take advantage of it and turn Sora into his Soul Jar. Metallix does give a "Ray of Hope" Ending by telling that Sora can vent the darkness in his heart, but it's still really shocking.
