Metroid II: Return of Samus is a sequel to Metroid NES, though chronologically it takes place after Metroid Prime 3: Corruption and before Super Metroid. Some time has passed since Samus Aran put a stop to the Space Pirates on Zebes and their plans to use the newly-discovered Metroids for evil purposes. To ensure this will not happen again, the Galactic Federation sends a research ship to the Metroid home world, SR388, to annihilate the species. When contact with the ship is lost, a rescue team and combat squad are sent, one after the other, to investigate, though none come back alive. Realizing the threat that the Metroids pose, the Galactic Federation sends Samus Aran on a mission to land on SR388 and destroy all Metroid organisms. With her experience on Zebes, the Galactic Federation is sure she will succeed.
Arriving, Samus lands her gunship at the base of an active volcano, near the only entrance where the Metroid lair can be found. She exits her ship and begins the difficult trek through the planet's dark network of caves and ruins.
One by one, Samus hunts down and destroys each Metroid on the planet. As she does so, she takes note of the steady mutation that each goes through. She discovers mutations which cause them to grow from their small jellyfish-like state into massive, hovering lizard-like beasts. Traversing deeper and deeper, the volcano rumbles at intervals and the lava drains, revealing a massive complex of Chozo ruins. Finally, after several harrowing battles with massive Omega Metroids, she uncovers a small ruined royal palace with infant, just born Metroids floating in the breeze. With their destruction, only one Metroid remains — the massive and deadly Queen Metroid. Samus fights a final battle before finally defeating the slithering monster, and as it crumbles to dust the final volcanic eruption sputters out. Returning to her gunship, Samus comes across a Metroid egg. The egg hatches and before her eyes a small Metroid hatchling floats out of the broken shell and begins to chirp at her. The Metroid, at seeing Samus first, believes her to be its mother. Samus, despite being ordered to exterminate the Metroids, spares its life. The two continue exiting the tunnels, and the Metroid hatchling helps Samus escape the caverns. Samus and the young Metroid board the gunship, ending the game.
On-board the gunship, Samus places the Metroid in a container so that it can't cause any harm to the ship. Noting the immense scientific opportunity that the captured hatchling poses, she departs SR388 and heads to Ceres Space Colony to deliver her groundbreaking find — a domesticated, infant Metroid.