METROID (NES)
Samus is sent to a planet where a new life species was found - the Metroids. They are stolen by Space Pirates for evil stuffTM. The Space Pirates go down, the Metroids survive.
METROID PRIME TRILOGY (GC, WII)
Prime (1): The Space Pirates are back somehow and use a substance called Phazon to do experiments on Metroids. Samus kills the head of the Phazon Metroids - Metroid Prime.
Prime 2 Echoes: Shortly before Metroid Prime died he made a copy of Samus out of Phazon. The real Samus has to alternate beetween the real world and a dark world to defeat Dark Samus.
Prime 3 Corruption: Samus defeats Dark Samus once more, destroying all the Phazon in the universe. Sadly, she triggers a Metroid epidemic while doing that.
METROID 2 (GAME BOY)
Samus is sent to destroy all the Metroids of the epedemic she triggered. Only one baby survives, and it thinks Samus is it's mother.
SUPER METROID (SUPER NES)
Scientists use the baby as energy resource, then it gets stolen. By the damn Space Pirates. In the final battle with Mother Brain, Samus is close to death, but the baby (now grown up) swoops in and sacrifices itself for Samus, and gives her it's power. Then Samus f***s up Mother Brain for good.
METROID OTHER M (WII)'s Intro Sequence is exactly the final battle of Super Metroid. And that's when the game begins.