In the Subspace Emissary mode, Princess Peach and Princess Zelda are captured by Petey Piranha, but one them is saved by Kirby. However, both of them are transformed into Trophies by Bowser afterward.
If Zelda got turned into a trophy by Bowser, Link and Yoshi eventually arrive to the Lake Shore and are continuing in their pursuit of the Halberd. Just as the False Zelda is about to fire the Dark Cannon at the pair, Mario and Pit slash the weapon in two, and the pair easily defeat the clone. However, just then, Link stops running and looks up to see Mario and Pit standing next to the trophy of the False Zelda, which begins to desintegrate. Thinking that Mario has destroyed the true Zelda's trophy, he rushes towards him and attacks Mario with his sword, which the plumber dodges. Link and Yoshi then engage in combat against Mario and Pit, but they lose and are turned into trophies.
Later Snake, Lucario and Meta Knight encounter the two princesses (still transformed into trophies), and fight with two evil clones of the princesses, one of the two being the false Princess Zelda. When the clones are defeated, the two princesses return to normal.
Ganondorf encountering the false Zelda and Peach characters