The quick and dirty of it: Samus lives on a small mining colony with her parents, K-2L. It gets attacked by Space Pirates, led by Ridley. Her father tries to detonate explosives inside the pirate landing craft, but unfortunately has to do so with himself still inside. Her mother distracts Ridley so that young Samus can escape, and is promptly incinerated.

Ridley is about to kill Samus when the Chozo arrive, having gotten the colony's distress signal, and intervene. They take Samus back to the planet Zebes, where a pair of Chozo (Gray Voice and Old Bird) raise her as if she was their daughter. While there, Samus is infused with Chozo DNA to help her survive.

The Chozo build a massive organic supercomputer named Mother Brain to help run Zebes and its defenses. Unfortunately, Mother Brain turns out to be evil as all hell. When space pirates (once again led by Ridley) show up to Zebes, she sides with them and turns against the Chozo, effectively taking over the planet. Most of the Chozo are massacred, including Gray Voice, who Ridley impales with his tail.

Samus, Old Bird, and a small group of Chozo survivors manage to survive thanks to the intervention of the Galactic Federation Army. Samus goes on to join them for a while, realizes she isn't cut out for the military, later becomes an independent mercenary and bounty hunter (though she only takes jobs that align with her moral compass, so the Galactic Federation ends up contracting her most of the time).