Battle Mode can be used to play against other people with a Nintendo DS using either DS Wireless Communications or Nintendo Wi-Fi Connection. While playing Battle Mode players will control either Link or three Phantoms. When playing as Link the player must explore the area and bring Force Gems back to their base. There are three different sizes of Force Gems, the heavier it is the harder it is to carry but the more points it rewards when brought back to the players base.
The player controlling the Phantoms must draw a path for each Phantom to try and move them towards Link. Safe Zones can be found throughout each level. When Link is standing in one he cannot be attacked by Phantoms and will not appear on the map of the opposing player. Once time runs out or Link is attacked by a Phantom the players will swap sides. After each player has played as Link three times the game will end. The battle can end before this depending on scores.
When exploring the area, Link and the Phantoms can obtain items to increase speed or attack, grant immunity to an attack, shuffle the location of all force gems, create a clone of Link, activate Wind Walls, and increase or decrease the amount of time remaining.
There are eight stages to choose from: Standard Large Stage, Standard Small Stage, Standard Tiny Stage, Inverted Stage, Back-to-Back Stage, Stronghold Stage, U-shaped Stage and Standard Medium Stage.
If the player reaches certain standards during a single Battle Mode match, the player will receive Big Plays. If the player obtains four different Big Plays, Link will receive a Golden Ship Part for the S.S. Linebeck from Fuzo on Cannon Island. Big Plays obtained can be viewed from the main Battle Mode menu.
|No Items||Win without using any power ups|
|No Dribble||Win without dropping a Force Gems outside a base or safe zone|
|Limit||Strike Link within the last 20 seconds of two rounds|
|Solo||Strike Link in any one turn using only one Phantom|
|Break||Break 10 or more of your opponent's helpful items|
|Take||Pick up 10 or more of your own helpful items|
|Perfect Master||Complete "Perfect" and "Limit" in the same match|
|Quick||Win a match, felling Link in the first 20 seconds of two turns|
|Miracle||Win with a final score of 1-0|
|Get Everything||Win, turning all the Force Gems your color|
|Guardian||Win without letting your opponent score any points|
|Perfect||Complete "Get Everything" and "Guardian" in the same match|
|No Miss||Win without being taken down as Link|
|Guardian King||Take Link down 3 times as the Phantoms|
|Master||Complete "No Miss" and "Guardian" in the same match|
|Battle Master||Complete "Limit" and "Master" in the same match|
In this game all players control Link at the same time while Phantoms are automatically controlled by the computer. Up to four players can play at once. Instead of carrying Force Gems back to bases, players merely pick them up. If a player is hit by a Bomb Flower or attacked by a Phantom, half of their force gems will be scattered onto the ground. The player with the most Force Gems in his possession at the end of the game is the winner.
Occasionally, Item Bubbles will appear which will grant Link one of four abilities: lightning that strikes nearby players, a pit opening around the arena, a shower of Force Gems around the player, or invincibility from Phantoms and the ability to damage opponents on contact for a limited time.
There are six stages to choose from: Ancient Earth, Frozen Plains, Fire Arena, Icy Plains, Scorched Battlefield and Shadow Stage.
|Bellum · Ciela · Linebeck · Link · Ocean King · Oshus · Tetra|
—Full list of characters
|Blaaz · Cyclok · Crayk · Diabolical Cubus Sisters · Dongorongo · Gleeok · Eox · Bellum · Ghost Ship · Bellumbeck|
|Bannan Island · Cannon Island · Goron Island · Harrow Island · Isle of Ember · Isle of Frost · Isle of Gust · Isle of Ruins · Isle of the Dead · Mercay Island · Molida Island · Zauz's Island|
—Full list of locations
|Temple of Fire · Temple of Wind · Temple of Courage · Ghost Ship · Goron Temple · Temple of Ice · Mutoh's Temple · Temple of the Ocean King|
|Oshus's Sword · Wooden Shield · Boomerang · Bombs · Bow · Bombchus · Grappling Hook · Hammer · Phantom Sword · Shovel · Fishing Rod|
|Leaf · Neri · Ciela · Pure Metals · Phantom Hourglass · Spirit Gem|
|Anouki · Deity · Fairy · Gerudo · Goron · Human · Hylian · Yook|
|Anjean · Byrne · Chancellor Cole · Link · Malladus · Princess Zelda|
—Full list of characters
|Stagnox · Fraaz · Phytops · Cragma · Byrne · Skeldritch · Demon Train · Chancellor Cole · Malladus|
| Fire Realm · Forest Realm · Ocean Realm · Sand Realm · Snow Realm|
—Full list of locations
|Forest Temple · Snow Temple · Ocean Temple · Fire Temple · Sand Temple · Tower of Spirits|
|Lokomo Sword · Rail Map · Recruit's Sword · Recruit Uniform · Spirit Flute · Spirit Tracks · Spirit Train · Stamp Book · Tears of Light|
|Boomerang · Whip · Whirlwind · Bow · Sand Wand · Bow of Light|
|Anouki · Demon · Goron · Hylian · Lokomo|