Here are five things Sonic Adventure 3's story reboot should explain
1. How Shadow survived
- Unbeknownst to him, Shadow's rings are power inhibitors placed on him by Professor Gerald. When Sonic took one off of Shadow's arm, it released enough power for him to be able to do a limited Chaos control to slow his fall just enough for him to barely survive the crash. The rules of Chaos control would be established as: Shadow and Sonic's ability to use chaos control is directly proportional to the amount of energy they have access to at the moment, including body energy, so they can use chaos powers naturally, but it's very limited without a chaos emerald. Also using them without an emerald takes away energy and tires them out proportionally to how much they use, so they must use these abilities strategically when using them without emeralds. The inhibitors not only hindered Shadow's powers, but also his memories so that he would have problems with his memories.
-alternate explanation: The similarity of him falling to Earth to the time after SA2 to the time before when he was falling in the escape pod, jolts all of his lost memories including his past life before Gerald found him which breaks the mental barrier to his powers that kick in when he is in grave danger.
2. The connection and similarities between Sonic and Shadow and their true origins
-Sonic and Shadow were both born as guardians to protect the planet. Sonic was born as a guardian since Shadow was incapacitated. Chaos from Sonic Adventure one was also one of these guardians. The Chaos Emeralds which were named after Chaos, the last known guardian to use them before Sonic, would have been made for the guardian(s) of Earth to use in times of great danger.
3. How Shadow was actually found by Gerald rather than made
- Shadow was part of a hedgehog tribe near the mystic ruins part of the planet. Gerald was looking for new specimens since the biolizard was needed life support thus was a failing when he comes across an unconscious Shadow and a destroyed landscape behind him recently done by Shadow. Gerald modifies two shock collar, restraining devices, that he was going to use on captured animals, and places them on Shadow's arms. Perhaps Professor Gerald was known for capturing animal specimens for research, and this inspired Eggman to capture animals. This is what he meant when he said his grandfather was his hero that inspired him. Shadow recovered from near death almost overnight showing he has amazing regenerative capabilities. This makes him the perfect specimen to use for research project Shadow, the research project on immorality.
Shadow's tribe got attacked by a band of thieves, and upon seeing many loved ones die his previously dormant guardian powers activate, and since it was too soon, he's goes on a rampage unable to control himself. This rampage created the pumpkin hill/red mountain/sky rail area, or at least happened over there.
4. Why the ARK was attacked and shutdown
-The main villain of the game, Freud Sigmund, was a fellow scientist and colleague of Professor Gerald that worked on the original project Shadow, the biolizard.
-Gerald was appointed head of project Shadow after finding Shadow, and convinces everyone except his rival Sigmund, that a field experiment proved successful creating Shadow.
- Sigmund convinces GUN to attack the ARK and shut it down because of Shadow the Hedgehog.
-After Gerald was executed Sigmund, was appointed to as the head scientist to oversee any further experimentation on Shadow, Sigmund uses this opportunity to absorb Shadow's regenerative energy allowing him to still be alive during Sonic's time. He creates an alternate persona to hide the fact his he could not have lived as long as he does and becomes a high up adviser and leader in GUN. He uses this position to manipulate and influence GUN's actions. He influenced GUN to capture Sonic in Sonic Adventure 2 even though clearly Shadow was behind the events.
5. How Gerald knew about the Chaos Emeralds and made artificial Chaos
It should be explained Professor Gerald and his team discovered the mystic ruins, and there learned of the Chaos Emeralds and Chaos, creating the artificial chaos off of his design.