Samus, after destroying Mother Brain, crash-landed back on Zebes after being attacked by Space Pirate fighters, and lost her Gunship and Power Suit. She was forced to infiltrate the Space Pirate Mother Ship in search of an escape vessel, and came across the escape-ship bay. However, she was unable to access it while suitless.
During the countdown sequence of the Mother Ship, Samus ended up back in the escape bay and fought off two Silver Space Pirates. A Zebesian was inside the Escape Ship about to fly off, but Samus quickly killed it and hijacked the ship, preparing to take off. Humorously, another Zebesian tried to jump on top of the ship, but was killed when it hit him.
What becomes of the Escape Ship is unknown. Samus has not been seen reusing this ship. In subsequent games, she uses her own Gunship, which is believed to have been her original ship, recovered from Zebes and refitted.