"My granddaughter Maria has always lived with me on the Ark. She was born here, but something was discovered that prevented her from going to Earth. You see, she has a fatal disease with no cure called Neuro-Immune Deficiency Syndrome, which gradually weakens all who have it and makes them very fragile. She could only look down on Earth and she longed to go there. I hoped to make a companion for her, a so-called Ultimate Lifeform in a desperate hope to cure my beloved granddaughter. My hope is that either the companionship can cure her or I can make a cure from the research. The other scientists on board the Ark thought it couldn't be done, so they named it "Project Shadow." I liked the name, so it stuck. I originally thought about experimenting on lizards, due to their ability to regrow their limbs. My prototype was far too dangerous, so I sealed it in the core of the colony. I then decided to design a hedgehog. However, I didn't have enough DNA, so I needed help. I made contact with a vessel called the Black Comet, owned by an alien race known as the Black Arms. Their leader, Black Doom, agreed to help. However, I didn't trust him, so I built a superweapon within the colony I called the Eclipse Cannon, in case he turned against me. I finally completed Project Shadow. Maria and Shadow got along better than I expected! However, I have not found a cure, and the government became aware of my plans. I sent them an ancient Gizoid robot I have been working on to buy some time, but I don't know how much longer I have before they shut down my operation by force…"

-Dr. Gerald Robotnik (recovered log entry) on Project Shadow

50 years ago, in the medical bay on Space Colony Ark…

Maria: Shadow…?

Shadow: Yes Maria?

*Maria looks down on Earth*

Maria: Do you think I will ever see Earth?

Shadow: Someday hopefully. Maybe we will go together.

*Shadow smiles, unaware that this will be his last smile for a very long time, and of the event that will change his life forever*

At that moment, G.U.N raided the Ark, aware of Gerald's experiment with immortality, and they discover, with the help of Black Doom, Project Shadow was completed. Shadow gets a comm message from Gerald

Shadow: What is it doctor?

*Shadow, for once, sounds panicked*

Gerald: I can't believe I'm saying this, Shadow. Grab Maria and run. To an escape pod. Head to Earth and get Maria into a hospital, where her medical treatments can continue. Go! Now!

Shadow: Heard you loud and clear. Goodbye, Doctor Gerald. Shadow out.

*Holding back tears, not wanting Maria to see him cry, he grabs her hand and runs. By the time they reach the stasis room, a G.U.N officer shoots Maria in the back, and she falls to the floor*

(Shadow) MARIA!

*She struggles and crawls to the stasis control panel. *She hits the button and Shadow is enclosed in the stasis tank*

(Shadow) Maria no!

*Shadow pounds on the glass*

(Maria) Sayonara, Shadow the Hedgehog…

*She hits a button and smiles*

(Maria) Protect Earth… bring hope to humanity…

*She shutters out her last breath and dies as Shadow is jettisoned from the Ark*

After news spread, Gerald, now in a lapse of depression and anger, reprograms the Biolizard and the Eclipse Cannon with the intention to destroy Earth, and shortly before he is executed, retrieves Shadow, and reprograms him to retrieve the Chaos Emeralds and bring them to the Ark. After being attacked by the Biolizard, they seal it, shut down all projects of Gerald's, and lock away Shadow's stasis tube. A hemisphere is built around the colony to make it appear as an asteroid and be forgotten by the public eye….

And the story begins 50 years later….