The Maria Mystery Conclusion

Based on my research, this is likely what happened:

Pre-invasion (50 years ago)

1. The BioLizard, a large creature with chaos control (but a primitive live-support system) is created. 
1. BioLizard is considered a failure. 
2. A historical experiment when on a rampage and nearly destroyed the Ark (Emerl). 
3. Prof. Gerald worked with Black Doom to correct his errors. 
1. Shadow is created. 
2. Child Commander spies and is shocked to see Black Doom. 
4. Maria befriended Shadow the Hedgehog. 
5. An outbreak of Artificial Chaos...caused Chaos. 
6. Due to various pressures, the United Federation decided to shut down the Ark and imprison or eliminate anyone involved with "Project Shadow."

The Doom

1. Maria ran with Shadow. 
1. (possibly helping fellow researchers or using heal units to gain GUN's trust).
2. At some point the two are nearly caught in one of the halls. 
2. Maria prepares to launch Shadow in escape pod to earth.
3. Maria is shot or injured. She says goodbye to Shadow. 
1. Shadow falls to earth in one of the pods. 
2. Maria dies.
4. The Professor is taken to Prison Island. 
1. Shadow is found and taken to Prison Island. 
2. Shadow is eventually put in suspended animation. 
3. Prof. Gerald is eventually executed.  

Present Time

1. Shadow is released but eventually remembers his promise. 
2. After a brush with death Shadow remembers little. 
1. Black Doom gives Shadow false memories to gain the hedgehog's support. 
3. Shadow (re?)remembers his promise. 
4. Shadow makes peace with the past.  

Shadow is one of the few characters to have a known background beyond the events of the games. It would be interesting to see this further expanded. On the other hand, Shadow letting go of the past was a wise move that prevented him from being used by others. Furthermore, Maria Robotnik hasn't appeared in the games since 2005. Ergo, seeing her again is unlikely.

Despite the different styles or stories, all end with Maria wishing the best for a world she never got to visit.