On her way to school, Freddi Fish meets with Luther, who brings his Codfish Commando action figure for show and tell.

Upon entering their classroom, Freddi and Luther learn from their teacher, Mrs. Croaker that their classmates saw a ghost, who stole their toys.

The game uses exactly the same mechanics as its predecessor, but contains newer puzzles, collectible and usable items, character encounters, locations, minigames and trivial click spots in the gameplay.

[6] Due to the common practice that adult women voice children of both genders, game designer Tami Borowick, who was behind the decision to make Freddi female during development of the first game, thought that players may not realize that Freddi was female and thus added a line in this game to clarify the character's true gender.

[7] Freddi Fish 2 was generally well-received, getting a 3-star rating from Allgame,[13] 9.5 out of 10 from Electric Playground,[8] 5 Stars from PC Magazine,[9] and Unikgamer gave a 7.5 out 10 score.