In the ending (or new beginning) of the game, the spot marked by the shining "X" is where the Isle of Ancients was. When Tabuu and the Great Maze were destroyed, most parts of our world returned to normal, but the effect of so many Subspace Bombs going off at once made it impossible for the Isle of Ancients to return to normal.
The taking of the battleship Halberd, as well as the scuffle between King Dedede and Meta Knight, were not shown in the game, because those scenes unfortunately had to be cut.
So that’s the inside scoop for you.
Hopefully, this post was able to shed a little light as to the motivations of the characters in the story.