The Metroid Fusion manual features the Journal of Samus Aran, a diary in which she details the events at the beginning of the game.
From the Journal of Samus Aran...Edit
SR388. A vile planet, former home of the Metroids. After so many years, the remaining creatures on this planet still seemed to be trying to recreate a natural hierarchy, one without Metroids at the top.
Biologic Space Labs was hired by the Federation to observe this restructuring of the ecosystem. And because of my experience on SR388, the Federation governor for this sector hired me to provide field assistance on the planet. So, once again I found myself drawn to that forsaken rock.
The biological sample collection was going smoothly on the planet's surface when I came into contact with an organism I had never before encountered.
The organism was an undiscovered, unnamed parasitic life form, which the researchers later called "X." Thinking little of it at the time, I boarded a ship and set out for the next collection point. Suddenly I felt my entire body seize up, and I lost consciousness. The ship began to drift away from planetary orbit toward an asteroid belt.
Thankfully, an auto-escape pod jettisoned me from the craft before the ship was destroyed. The researchers in the newly-constructed research station orbiting SR388 sent a shuttle to recover the pod shortly thereafter. However, in the time since my infection, the X had multiplied rapidly in my body and had even infected my Power Suit.
My heart rate and blood pressure dropped rapidly as I fell into a deep coma. The Onboard Medic Simulation predicted only a 0.873% prognosis for survival. I was transported to Galactic Federation HQ for emergency medical treatment.
The fact that the Power Suit contained biological components and was also integrally connected to my body seemed to worsen the matter. The Federation surgeons were unable to remove the suit while I was unconscious. Their only choice was to cut and remove parts of the infected suit from my still-unconscious form; immediately after, they sent the suit parts to the Biologic Space Labs research station for study.
Even with the parts removed, however, the X infection was spreading rapidly through my nervous system, and the researchers monitoring my deterioration knew of no cure...
Someone proposed a desperate treatment: create a vaccine from Metroid cells. Apparently the Federation had preserved a cell culture from the last Metroid. The scientists quickly prepared and administered the vaccine. The symptoms of the infection disappeared instantly, and all of the X parasites within me died in moments. I am still amazed by the serendipity of this result...
When I woke, the scientists told me that the hatchling had saved me once again.
Almost immediately after I awoke, we received a distress call from the research station.
Emergency! Explosion of unknown origin in the Quarantine Bay!
The screams from the com receiver were loud enough for me to hear even in the infirmary. I knew that something terrible was about to happen... was already happening. I immediately boarded the ship the Federation had provided me and sent a reply message: