Navi Trackers (originally planned as a standalone game titled Tetra's Trackers) is only included in the Japanese and Korean versions of The Legend of Zelda: Four Swords Adventures. The game was inspired by Marvelous: Another Treasure Island, a SNES game directed by Eiji Aonuma. Multiple players, using a combination of the television screen and Game Boy Advances, search for members of Tetra's pirate gang to gain stamps from them, as many as possible within a given time limit. Unlike most other entries in the series, players can select their gender as well their name; however, they play as one of the Links regardless of this choice. Tetra and her pirate crew have full voiceovers in place of text-only dialogue, with Tetra also synthesizing the two-character name that each player inputs at the beginning of the session, possibly why this game was not localized for the English release.

The Navi Trackers mode in The Legend of Zelda: Four Swords Adventures started life as a remake of Marvelous: Mouhitotsu no Takarajima, a Japan-only RPG for the Super Famicom. In a 2004 interview with Nintendo Online Magazine, director Yoshinori Tsuchiyama stated that its rebranding as a Zelda game was the result of "the desire to make a complete departure from Hyrulean Adventure, and to incorporate a sense of realism produced by having the game talk to the players through the screen." Tsuchiyama, co-director Toshiaki Suzuki, and series producer Eiji Aonuma previously worked on Marvelous: Mouhitotsu no Takarajima. Because of these circumstances, The Legend of Zelda: Four Swords Adventures contains unused assets for the Marvelous remake in its code, including icons, backgrounds, cursors, and a 3D model for Gina (whose role is filled by Tetra in the final game).