Chell is long gone from Aperture, the BSL station is destroyed, and GLaDOS is bored of the co-op testing initiative.

"Samus, we the Galactic Council find you guilty of going against orders. Though on the account of your ship's AI, Adam, you did so to save all of galactic civilization. Still no matter the good you are hereby sentenced to five years imprisonment to the Aperture Science Enrichment Center. Your ships AI will be going with you, however your progress will be monitored remotely."

Samus lowered head in acceptance as she knew that her real sentence was death because everyone who had been sentenced to imprisonment at the ASEC wound up dead. She was cuffed and taken from the council trial and loaded into a prison transport that bore the logo for the Enrichment Center. She felt defeated but she would stay strong, she made a promise to Old Bird many years ago and she still had to fulfill that promise. "Keeping the galaxy safe from disaster." Samus muttered to herself as the transport vessel hummed to life.

The trip itself was very uneventful leaving Samus to her thoughts. She thought back to her missions over the years and was rather grateful for some of them but others just brought a stale taste to her mouth, while others made her want to vomit out right. "Ugh if I EVER see Phazon again, it will be too soon." she said at the thought.

After what seemed like several hours they arrived at the place but the vehicle had stopped at least one hundred yards from the facility itself. Samus was practically tossed from the transport just moments before it swiftly turned around and sped away. She stood there staring at the white-washed walls of the facility in the distance. Swallowing her pride and ignoring what she really wanted to do she made her way towards the facility.

Upon getting within ten yards of it the ground beneath her feet fell in and she began to fall. The shackles that bound her hands and feet were rattling in the air as she attempted to break them. It seemed like an hour but it was just a few minutes till she hit the ground straight on back first. The wind got knocked out of her and she passed out. The last thing she saw before her vision fully faded away were two robots that picked her up and carried her off somewhere.

"Oh a new subject has arrived. I hope that this one will do better than the last one. The co-op testing initiative did far better than they did. That fat slob barely made it past the first chamber... until they fell into the acid." GLaDOS said as she looked at the security camera feed.

Well there is the prologue hope you Portal and Metroid fans like this start. Also I note that this intro bit is rather short. can't be helped really.