The player controls a hunter that they can name, supported by an assistant handler, who are a part of the Fifth Fleet which has been summoned by the Research Commission to provide more support to the New World. A particular focus of the Expedition is to study Elder Dragons, powerful beasts that can affect entire ecosystems, and why they migrate to the New World every ten years in an event known as the Elder Crossing. While traveling to the New World, the Fifth Fleet encounters Zorah Magdaros, a massive Elder Dragon the size of a mountain. After being rescued and arriving at the base camp, known as Astera, the Hunter and their Handler undertake various tasks to explore the area and study Zorah Magdaros at the behest of the Commander of the Expedition. The Expedition determines that Zorah Magdaros is dying and is migrating to a massive graveyard, known as the Rotten Vale. An Expedition-led capture mission against Zorah Magdaros is foiled by Nergigante, an Elder Dragon that feeds on other Elder Dragons, and is protecting Zorah Magdaros as its future meal. After escaping the ambush, Zorah Magdaros unexpectedly enters the Everstream rather than traveling to the Rotten Vale. After further investigations, the Expedition learns that if Zorah Magdaros dies within the Everstream, its released bio-energy will destroy the New World. With no time to evacuate, the Expedition develops an emergency plan to intercept Zorah Magdaros and drive it to the ocean, where its released bio-energy will form a new aquatic ecosystem. Nergigante once again interferes, but this time is driven off by the Hunters, and Zorah Magdaros is successfully driven into the ocean.