Unused code in the files of the GameCube version contains eight different weapons that were considered or almost finished including a Claymore, a Torpedo Launcher, and a Mustang Viper.
The idea of not having "item boxes" in the game was based on "Sweet Home". The team wanted to remove it, so that it would feel a lot harder to play.
It was revealed that what looks like a Mega Man Starforce costume, seen from a picture taken by Game Informer, was only a placeholder costume for when Mega Man equipped Tundra Storm's weapon during development.
Unused text in the GBA version's files suggest that all of the in-game spells (except for Expelliarmus) were planned to be upgradeable.
Unused code for the "Scribble HUD," "Super Power Recharge," and "Thermographic Spectrafier" can be found in the GameCube and PlayStation 2 version's files, suggesting these may have been planned to be power ups.
The SHC squirrels originally held a green Walkie Talkie in the It's War chapter. While it isn't present in the game under normal circumstances, it can be restored via a hacking device.
An unused laptop can be found in the game's files. The screen on the laptop says "Look sad people. Get a life now."

There was a weapon that was supposed to be used in the game called the "Revolverator", but it was cut off from the game. According to game designer "Corey Stockton", when you find a colorless Revolverator in the "Insomniac Museum" from "Ratchet & Clank: Going Commando", he said:
"You may recognize this drill from Ratchet and Clank 1. It was held by a "large construction worker (The Miner from Hoven)" who gives you a lump of Raritanium. This was originally a weapon called the Revolverator. Ratchet would strike enemies with it and then spin them over his head with the drill bit. Unfortunately, this ended up leaving Ratchet open for attack, and also required a lot of resources to pull off, so it was cut."
"You may recognize this drill from Ratchet and Clank 1. It was held by a "large construction worker (The Miner from Hoven)" who gives you a lump of Raritanium. This was originally a weapon called the Revolverator. Ratchet would strike enemies with it and then spin them over his head with the drill bit. Unfortunately, this ended up leaving Ratchet open for attack, and also required a lot of resources to pull off, so it was cut."
In the 3DS version's files are unused models from the "Cook Kirby" Final Smash from Super Smash Bros. Brawl.
Early footage of the game showed The Hand boss having destructable tombstones in the arena which are not present in the retail release. The Hand also had a different death animation.

Like its predecessor, Super Smash Bros. Melee, The game was originally supposed to include alternate trophies along side their regular trophies for the playable characters. No icons nor preview images exist for any of the trophies.
At one point in development, the player was able to acquire a space suit which would allow Duke to traverse areas in space without dying.
All of the characters who only appear as opponents in Story Mode have a bullet for whenever they get shot by Erron Black's X-Ray move. Normally these are stored in character DISM files, but the Story Mode characters have their bullets located within their character packages.
There are eight items that were given away as part of a promotional event held by The 7-Eleven chain of convenience stores in Japan.
The following items are inaccessible through normal play outside of Japan, where the promotional event was held.
•Seven Sword
•Eleven Shield
•Boiled Chicken
•Spicy Chicken
•Chicken Link
•Mille Crepe
•Moist Bread
•Pure Honey
The following items are inaccessible through normal play outside of Japan, where the promotional event was held.
•Seven Sword
•Eleven Shield
•Boiled Chicken
•Spicy Chicken
•Chicken Link
•Mille Crepe
•Moist Bread
•Pure Honey

The "Korok seeds" in this game originally started out as being rock-like objects that players were meant to discover throughout their adventure. These rock-like objects used the Master Sword pedestal asset from The Legend of Zelda: Skyward Sword.
The game includes unused graphics for miniature versions of the unknown soldiers, most likely intended to be used as extra lives or other bonus pickups.

There is an unfinished and unused outfit remaining in the game's data, that gives Link a pair of Great Fairy wings, prosthetic antennae, and a Kokiri-like tunic. It appears to be from an early stage in development since it has Link's hair and body proportions from A Link Between Worlds, with the "Toon Link" facial features used in Tri Force Heroes.
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