* The ending: It appears it was AllJustADream, but then [[spoiler: [[OrWasItADream Link finds the titular Hourglass and rushes to the other side of the ship JUST IN TIME to see Linebeck's ship on the horizon]]]]. (The music probably didn't help, either.) Just imagine it now, how [[spoiler: [[JerkWithAHeartOfGold Linebeck]] must have been looking back to Link, saying "You did good, kid."]]
* As divergent from the game as the manga of ''Phantom Hourglass'' was, they still did good with the scene where [[spoiler:Linebeck is possessed by Bellum. He would rather kill himself than attack Link, and it's the only means of defiance he has.]]
* At some point during the game, you get a letter in the mail from Linebeck. Seems strange at first since he's always travelling with Link, until the letter reveals that despite the way he usually acts, Linebeck really is grateful towards Link. He just finds it hard to actually say that to him.
* When Link is forced to bid Ciela farewell, he reaches out to touch her one last time, and Ciela responds by gently resting herself in his hand. It's especially so considering [[FutileHandReach the last time]] he tried doing this to say goodbye to a companion.