This is the prelude of Journey to Death.
Samus was in the gunship provided by the Galactic Federation to reach BSL. After having several missions on there, she sent it into SR-388 to prevent the X from infecting the galaxy.
Samus spotted a Space Pirate frigate in space heading for her. She quickly piloted the ship onto one of its docking bays, and got out so quickly that she barely heard Adam say "Good Luck". She went through the frigate, killing Space Pirates in her path, until she reached the command bridge.
In the command bridge, there were several black space pirates like the ones in lower Norfair. She killed each of them, not without a little beating though. She noticed this wierd thing on the floor, and scanned it. It turned out to be harmless and Samus took it, deciding to study it later.
She went to the Reactor Core, killed the Gold Pirates and Black Pirates there, and shot several super missiles straight into the reactor core, causing an explosion and causing the frigate to start to blow up. Samus quickly went back to her ship and flew away.
"Good job, Samus", Adam said. "What is that you have?" Samus pressed the button on the device she found back on the frigate. A hologram came out of the device. "RIDLEY!" Samus screamed. "Hello Samus" Ridley said. "We Space Pirates have placed several bombs in the cores of several planets, like Norion for example, and when they blow up, the planets will too. If you tell them, we blow them up immediately. However, if you come to the Space Pirate Homeworld we will not activate the bombs. However, leaving the planet afterwards is out of the question. You have 48 hours to get here." Then the hologram turned off.
"You aren't going, are you Samus?", Adam asked. "I must. I have no choice." Samus said in return.