After exterminating the Metroids on SR388 in Metroid II: Return of Samus, Samus Aran brings the infant Metroid to the Ceres Space Colony, likely staying at the colony while scientists study the young metroid. The scientists' findings show that the powers of Metroids could be harnessed for the benefit of mankind. Leaving the Metroid in their care, Samus leaves Ceres in search of a new bounty to hunt. However, shortly after leaving, Samus picks up a distress call from Ceres and returns to investigate. As Samus explores the space colony, she finds the power is out and eventually finds bodies lying about the room that contained the Metroid. She continues investigating and meets Ridley once again — holding the container with the Metroid inside in his claws. Samus and Ridley fight, though Ridley flies out of the station. At the same time, a countdown begins, showing Samus has 60 seconds before the station explodes. Samus quickly returns to her gunship and flies to the nearby Zebes in pursuit of Ridley.
The Space Pirate base that was destroyed in the first Metroid game has now been rebuilt. It should be noted that a whole section of Crateria, the first section of Zebes, looks like Tourian from the Metroid (dubbed Old Tourian), with Mother Brain's old control chamber inferring that it is the remains of the Space Pirate base from the original Metroid. Samus sets out to locate the infant Metroid and prevent the Space Pirates from gaining use of its powers. As in the previous games, Samus is forced to delve into the planet through its many caverns to hunt down the Space Pirates. This time, however, Samus can only enter Tourian by destroying four bosses: Kraid, the giant lizard whose base makes up a large part of Brinstar; Phantoon, an entity that controls the destroyed Wrecked Ship and reroutes its power supply to Mother Brain; Draygon, a crustacean monster that occupies a submerged pirate lab in Maridia; and Ridley himself, who controls Norfair and his lair.
After defeating all four of the bosses, and finding Mochtroids, unsuccessful clones of Metroids, Samus battles her way through Tourian, encountering newly bred Metroids. After passing through several corridors filled with Metroids, she encounters a Metroid larger than the rest. Before she attacks it, the giant Metroid drains 99.9% of her life force. However, it seems to recognize Samus; it appears that this huge Metroid is the infant taken from SR388. According to the Nintendo Power Player's Guide, the huge Metroid is named "Super Metroid".
After the Metroid departs, Samus recovers her energy and confronts Mother Brain. After Samus destroys the creature's stasis tank and inflicts enough damage, Mother Brain attaches itself to a giant mechanical body and the battle begins again. During the battle, Mother Brain uses a massive burst of energy from its eye, nearly destroying Samus. Samus finds herself unable to move while Mother Brain charges up to finish her off. Before the final blow can be inflicted, however, the once Infant Metroid suddenly attacks Mother Brain, draining its energy until it appears dead. The Metroid then attaches itself to Samus and begins feeding its energy to her. However, Mother Brain soon recovers and begins firing upon the hatchling, weakening it until it lifts off of Samus. A final shot destroys the hatchling, leaving its remains to fall upon Samus.
Pulsating with energy from Mother Brain, Samus now possesses the almighty Hyper Beam. With it, she easily destroys Mother Brain, who falls to the floor and turns to dust. This in turn triggers a self-destruct sequence, giving Samus three minutes to escape through the emergency evacuation shaft of the original base. Along the way, Samus rescues several Etecoons and a Dachora and makes it to her gunship just in time and takes off, watching the planet explode in a flash of light.

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.

Metroid on the NES was one of the first games to give off real challenge like the Legend of Zelda. There was nothing wrong with this game. There are 3 stages to the game: Brinstar, Norfair and Tourian. There are 3 bosses in the game: Kraid, Ridley and Mother Brain. There are 5 possible endings to Metroid, all featuring Samus in various stages of un-dress: The slowest time featured an ending were Samus turns her back towards the player. The second slowest time featured an ending were Samus in her Power Suit waves to the player. The middle time featured an ending were Samus removes her helmet. The second fastest time featured an ending with Samus in a leotard, and the fasted time featured an ending with Samus in a bikini. After that the game restarts and the player keeps most of the power ups they collected during the previous game and Samus with a leotard of bikini, witch ever the unlocked. There are also "hidden worlds" thought to be for the best of players, and it involves the trap hatch glitch were the player can become stuck in the door. Once activated the player can jump through the wall and into various rooms filled with several, indestructible enemies including Zoomers and Mother Brains. The JUSTIN BAILEY password was a password that was not intended for use in the game. When used the player starts as leotard Samus at the elevator between Brinstar and Norfair. The NARPAS SWORD0 000000 000000 code was a code purposefully built into the game that starts the player at Brinstar with the Varia Suit, 255 missiles even though the maximum is 205. The player is indestructible and will go to 39 health when they reach 29. The player starts with the Wave Beam, though when it hits it has a similar effect as the Ice Beam. In conclusion Metroid has the greatest plot and game play OF THEM ALL!!!!!!!!!!!!!!!!!!!!!!!!