The plot stays largely faithful to Metroid II, now opening with a Super Metroid-style introduction narrated by Samus Aran about the nature of her mission on SR388. As the game unfolds, Samus's scanners automatically download Logbook entries — much like the Metroid Prime series — that flesh out the lore of the planet's areas and bosses. She can also uncover optional sites, among them the landing spots of the G.F.S. Thoth and an Anhur-class patrol ship carrying two ill-fated Galactic Federation teams that had been sent to rescue an earlier Special Squadron — resting places Metroid II mentioned in its manual but never actually depicted.
Along the way, Samus comes across surviving Federation Marines battling a Zeta Metroid that morphs into an Omega Metroid before killing them with ease; there's no way to save them. The mysterious earthquakes tied to the Metroids' deaths are implied to be the work of the Queen Metroid herself, whose cries echo during the final few kills, and the Logbook reveals that the cave system sits between two tectonic plates on SR388. The game ends with Samus wiping out the last of the Metroids and the Queen, then discovering an infant Metroid she comes to call "the baby." After the credits, she speaks Super Metroid's famous opening line — "The last Metroid is in captivity. The galaxy is at peace." — and in the best ending is seen in her Gunship calling the Space Science Academy about the baby, leading straight into Super Metroid.