You COULD make the same story completely original! Something like:
After the B.S.L. incident, Samus was put on trial. However, Samus (had a top-notch lawyer/was able to fully explain what happened on the station). The Federation decided only to give Samus less important missions. They had her collect some virus like liquid they discovered which also had a few properties of Phazon. While Samus was collecting, however, she was ordered to head back to H.Q. When she got there, she discovered the place was deserted. Suddenly, the alarm started ringing. Samus raced back to her ship and left H.Q. just as it exploded. Unfortunately, a peice of debris struck the ship and damaged main engines AND thrusters, causing a hyper drive spark to send her crashing into an unkown planet full of the liquidy-phazon-virus-stuff. She was okay, but got infected and lost most of her abilities...
Edit: Gah! Repetition in the third sentence! Fix'd.
Edit 2: Liquid spelt wrong. >.>