The valley is the site of three major battles that occurred in the War Across the Ages. The first time is when the heroes and the Hyrulean Army confront the black sorceress Cia for the first time to close the Gate of Souls where monsters are swarming from. The mission is a failure, however, when Cia steals the Triforces of Courage and Wisdom from Link and Sheik respectively and opens more Gates of Souls across three significant time periods in Hyrule's history.
The second time is when the bolstered and morale-driven Hyrulean Army, this time joined by individuals across the ages, return to the Valley to force a final confrontation with Cia. The final time is when the armies commanded by the Demon King Ganondorf invade the Valley to take the Triforce of Power, which had fallen into Lana's possession after Cia's disappearance.
Prior to its English name being revealed, the unofficial name of this location was Lanayru Valley.
The Valley of Seers returns as a stage. In the game's version of March of the Demon King, the Valley of Seers has a clear blue sky, likely to reflect the fact that it is under Lana and the Hyrulean Forces control following Cia's defeat.
While not an actual playable stage in the storyline based on The Wind Waker, the location appears in the beginning of the arc, as Lana is still trying to search for Cia's whereabouts due to her vanishing, only to end up ambushed by an unidentified evil force with her Triforce of Power being stolen as a result.